<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">I think that it is more important what people have written about this topic, rather than spending time in expressing personal opinion.<br><div>Lots of nice readings out there.</div><div><br></div><div>I can recommend this paper:</div><div><br></div><div><a href="http://pubs.acs.org/doi/pdf/10.1021/ct1005455">http://pubs.acs.org/doi/pdf/10.1021/ct1005455</a></div><div><br></div><div>It's about "<span class="Apple-style-span" style="color: rgb(26, 26, 24); font-family: Helvetica; font-size: 13px; "><b>Long-Range Electrostatic Effects in QM/MM Studies of Enzymatic Reactions: Application of the Solvated Macromolecule Boundary Potential "</b></span></div><div><font class="Apple-style-span" color="#1A1A18" face="Helvetica" size="3"><span class="Apple-style-span" style="font-size: 13px;"><b><span class="Apple-style-span" style="color: rgb(0, 0, 0); font-family: 'Helvetica Neue'; font-weight: normal; font-size: medium; ">This is a very good work by Thiel and coworkers of 2011.</span></b></span></font><div><div><br></div><div>Another good one is:</div><div><br></div><div><a href="http://pubs.acs.org/doi/abs/10.1021/ct049941i">http://pubs.acs.org/doi/abs/10.1021/ct049941i</a></div><div><br></div><div>It's about "<span class="Apple-style-span" style="font-family: 'Trebuchet MS', Arial, Helvetica, sans-serif; font-size: 18px; font-weight: bold; line-height: 25px; ">An Efficient Linear-Scaling Ewald Method for Long-Range Electrostatic Interactions in Combined QM/MM Calculations</span><span class="Apple-style-span" style="font-family: 'Trebuchet MS', Arial, Helvetica, sans-serif; font-size: 18px; font-weight: bold; line-height: 25px; "><span class="Apple-style-span" style="font-family: 'Helvetica Neue'; font-weight: normal; line-height: normal; font-size: medium; ">"</span></span></div><div>by Darren (York) and coworkers of 2006.</div><div><br></div><div>Starting from these papers you can find extremely useful information in the therein cited references.</div><div><br></div><div>Teo</div><div><br></div><div><br></div><div>On Aug 4, 2011, at 2:03 PM, marco.stenta wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>OK:<br>the periodic stuff was another question, unrelated to the box<br>recenter.<br>My question was whether a (non periodic QM)/MM simulation is<br>acceptable for publication nowadays.<br>In that case I can put some effort and try to learn how to setup a<br>full periodic system, if it is really worth.<br>I want to avoid being unable to reply to a referee criticizing my<br>1milion hour - long simulation because it is not fully periodic.<br>I've seen in the past non periodic was common, but what now? CP2K seem<br>a pretty powerful tool and I would know your personal educated opinion<br>about that: is a (non periodic QM)/MM reaction study (TI Metadynamics)<br>prone to criticism for that or not?<br><br>thanks a lot<br><br>m<br><br><br><br>On 4 Ago, 12:43, Teodoro Laino <teodo...@gmail.com> wrote:<br><blockquote type="cite">We provide suggestion: finally you need to do things at your own convenience.<br></blockquote><blockquote type="cite">Having said that:<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><blockquote type="cite">so what should I do with the XC_grid section?<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> &XC_GRID<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> XC_SMOOTH_RHO NN50<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> XC_DERIV SPLINE2_SMOOTH<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> &END XC_GRID<br></blockquote></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><blockquote type="cite">Do you suggest removing it altogether ?<br></blockquote></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">It's your decision: you found two different posts, analyze them, do tests (!) and draw your conclusions.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><blockquote type="cite">what about EPSFIT?<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">now the defaults is 1.00000000E-04<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">but here it was suggested to use 10^-2<br></blockquote></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><blockquote type="cite"><a href="https://groups.google.com/group/cp2k/browse_thread/thread/dfdde2aa4b6">https://groups.google.com/group/cp2k/browse_thread/thread/dfdde2aa4b6</a>...<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">which is the most accurate?<br></blockquote></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">EPSFIT regards GAPW only. You're using GPW. Why are interested in that?<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><blockquote type="cite">Then another point:<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">I'm familiar with QMMM where the QM is not periodic.<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Do you suggest me to switch to a periodic description? I is a standard<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">enzymatic system on which I will study a reaction mechanism with TI<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">and metadynamics: are the results obtained with a (non-periodic QM)/<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">MM simulation acceptable?<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">What do you usually do in such cases?<br></blockquote></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">I've never talked in my reply (to your message) about periodic or non-periodic. I've only said that you should try to:<br></blockquote><blockquote type="cite">-) switch off the translation/centering of the QM system<br></blockquote><blockquote type="cite">-) use an NVE to inspect the energy conservation<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">the translation/centering of the QM system does not depend on the periodic or non-periodic. It depends on the fact that the density is contained in a simulation box and cannot travel freely around space.<br></blockquote><blockquote type="cite">Moreover, since you have QM atoms moving, the center of QM system will be constantly moved in the center of the QM box and this creates the drift.<br></blockquote><blockquote type="cite">Periodic / non-periodic is a totally different story and is not affecting the conserved qty with a constant drift (maybe in another way).<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><blockquote type="cite">I'll definitely check with an NVE for the energy conservation.<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">but how can I assess later equilibration in my NVT system if the<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">conserved quantity still drifts? is the sum of kinetic and potential a<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">good parameter? RMSD of the forces of the active site?<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Is conserved quantity a parameter to worry about?<br></blockquote></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">What about the conserved quantity printed in the .ener file (second-last column)? That contains everything..<br></blockquote><blockquote type="cite">If it drifts there is a problem with your setup. In this case, as I said, very probably is the continuous translation/centering of the QM system.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Teo<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><blockquote type="cite">Any suggestion based on your experience is welcome<br></blockquote></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><blockquote type="cite">thank you very much in advance<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">marco<br></blockquote></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><blockquote type="cite">On 4 Ago, 09:29, Teodoro Laino <teodo...@gmail.com> wrote:<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">My hypothesis: The very basic answer is that your QM system is continuously translated in the middle of the QM box.<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">You say that you keep all the QM atom frozen. In the input file you've sent I don't see that (i.e. it is commented, modulo my personal mistakes in looking at an input of 300 lines!). So I do not think that you are really keeping all QM atoms frozen. This translation is definitely accounting for a constant drift (it's quite normal to observe in PW based codes).<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">You can try to disable the translation and see what happens.<br></blockquote></blockquote></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">XC_SMOOTH_RHO may also lead to a non-perfect energy conservation. Why are you using that?<br></blockquote></blockquote></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">There could be of course other reasons.. but.. let's proceed stepwise..<br></blockquote></blockquote></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Regarding the cons. Qty, It should be clear that in an NVT ensemble (compared to NVE) the conserved quantity is not only the sum of the kinetic and potential energy of the particles, but you need to include as well the thermostat energies (which are not printed in the ener file)<br></blockquote></blockquote></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">The Cons Qty (i.e. including the thermostat energies) is the quantity which should be conserved.<br></blockquote></blockquote></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">As a side comment: if you're curious about your energy conservation just run a simple NVE. In this case you are summing too many effects that (I kind of reckon) you can't control very well.<br></blockquote></blockquote></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Regards,<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Teo<br></blockquote></blockquote></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">On Aug 4, 2011, at 9:06 AM, marco.stenta wrote:<br></blockquote></blockquote></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Dear all,<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">I have a question for any QM/MM user/developer.<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">I have a NVT simulation of a big protein embedded in a water box,<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">already equilibrated at MM level, and then 2 ps were performed by<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">keepign the heavy QM atoms frozen, as to further relax the MM atoms<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">surrounding the active site.<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">*the system contains a couple of Mg atoms (Mg: TZVDD3DF3PD-GTH-BLYP<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">all the other atoms DZVP-GTH-BLYP)<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">*charge of the qm system is -1, the spurious charge left on the MM<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">part was somehow redistributed/adjusted as to have<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">CHARGE_INFO| Total Charge of the Classical<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">System: 0.000006<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">*QM is not periodic and MT is used as poisson solver for the QM part<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">(the box was chosen to be 2.5 times the size of the QM part, which is<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">globular and compact)<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">* the cutoff was set to 320 and the grid is COMMENSURATE<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">*the parameter XC_SMOOTH_RHO NN50 was also set<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">*H are substituted with D, and the timestep is set to 0.2 fs<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">(the full input is attached below)<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">what troubles me is the drift in Cons Qty.<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">I understand I can still be out of equilibrium and the system should<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">further relax, but in similar simulations I observed a constant drift.<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Moreover the Cons Qty[a.u.] is not the sum of potential and kinetic<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">energy (.ener file): is this OK? or it is a bell ringing for<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">something deeply wrong in my calculation/setup/input/system?<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">cons qty -(pot + kin) = err<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">step 1: -1517.083028953-(-1747.938628518+230.841109714) = .<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">014489851<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">step 203: -1517.034195266-(-1747.682577807+230.042654659) = .<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">605727882<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Thansk a lot<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Marco<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"># Step Nr. Time[fs] Kin.[a.u.]<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Temp[K] Pot.[a.u.] Cons Qty[a.u.] UsedTime[s]<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"> 0 0.000000 230.867136550<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">300.555492024 -1747.950286957 -1517.083150407<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">0.000000000<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"> 1 0.200000 230.841109714<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">300.521608861 -1747.938628518 -1517.083028953<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">399.900000000<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"> 2 0.400000 230.807655637<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">300.478056511 -1747.928456404 -1517.083062027<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">134.000000000<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"> 3 0.600000 230.730159995<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">300.377168437 -1747.920690429 -1517.082994355<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">130.840000000<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"> 4 0.800000 230.740950337<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">300.391215894 -1747.914613364 -1517.081103127<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">130.830000000<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"> 5 1.000000 230.761638258<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">300.418148564 -1747.914568012 -1517.081032391<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">134.510000000<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"> 6 1.200000 230.746886303<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">300.398943661 -1747.920038506 -1517.081850762<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">134.440000000<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"> 7 1.400000 230.781912025<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">300.444542065 -1747.929605498 -1517.082015560<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">130.700000000<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">.<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">.<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">.<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">.<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">.<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"> 198 39.600000 230.304901871<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">299.823544102 -1747.846813641 -1517.033160667<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">132.440000000<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"> 199 39.800000 230.235992906<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">299.733834635 -1747.807562871 -1517.033321937<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">122.030000000<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"> 200 40.000000 230.132127496<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">299.598616952 -1747.770362015 -1517.033673946<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">125.460000000<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"> 201 40.200000 230.145587240<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">299.616139584 -1747.737129241 -1517.034724628<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">134.050000000<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"> 202 40.400000 230.026559444<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">299.461182675 -1747.707292580 -1517.034666102<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">125.710000000<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"> 203 40.600000 230.042654659<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">299.482136309 -1747.682577807 -1517.034195266<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">125.570000000<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">###########################################################################################<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">MY INPUT:<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">@SET NSTEPS 500000<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">@SET SOLNAME MOL69<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">@SET QMCHARGE -1<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">@SET QMPOISSON MT<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">@SET FREQ 1<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">@INCLUDE boxes.inc<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">&GLOBAL<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"> PRINT_LEVEL LOW<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"> PROJECT system<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"> PROGRAM CP2K<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"> RUN_TYPE MD<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"> WALLTIME 21000<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">&END GLOBAL<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">&MOTION<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"> &MD<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"> ENSEMBLE NVT<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"> STEPS ${NSTEPS}<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"> TIMESTEP 0.20<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"> TEMPERATURE 300.0<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"> &THERMOSTAT<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"> TYPE CSVR<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"> REGION DEFINED<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"> &DEFINE_REGION<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"> MM_SUBSYS ATOMIC<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"> &END DEFINE_REGION<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"> &DEFINE_REGION<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"> QM_SUBSYS ATOMIC<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"> &END DEFINE_REGION<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"> &CSVR<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"> TIMECON 50<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"> &END CSVR<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"> &END THERMOSTAT<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"> &PRINT<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"> FORCE_LAST T<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"> &ENERGY<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"> &EACH<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"> MD 1<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"> &END EACH<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"> FILENAME =system.ene<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"> &END ENERGY<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"> &END PRINT<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"> &END MD<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"> &PRINT<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"> &TRAJECTORY SILENT<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"> &EACH<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"> MD ${FREQ}<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"> &END EACH<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"> FILENAME =system.dcd<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"> FORMAT DCD<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"> &END TRAJECTORY<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"> &VELOCITIES OFF<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"> &EACH<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"> MD ${FREQ}<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"> &END EACH<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"> FILENAME =system.vel<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"> &END VELOCITIES<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"> &FORCES<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"> &EACH<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"> MD ${FREQ}<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"> &END EACH<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"> FILENAME =system.for.DCD<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"> FORMAT DCD<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"> &END FORCES<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"> &RESTART_HISTORY OFF<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"> &END RESTART_HISTORY<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"> &RESTART SILENT<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"> ADD_LAST NUMERIC<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">...<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">leggi tutto<br></blockquote><br>-- <br>You received this message because you are subscribed to the Google Groups "cp2k" group.<br>To post to this group, send email to <a href="mailto:cp...@googlegroups.com">cp...@googlegroups.com</a>.<br>To unsubscribe from this group, send email to <a href="mailto:cp2k+uns...@googlegroups.com">cp2k+uns...@googlegroups.com</a>.<br>For more options, visit this group at <a href="http://groups.google.com/group/cp2k?hl=en">http://groups.google.com/group/cp2k?hl=en</a>.<br><br></div></blockquote></div><br></div></body></html>