<p dir="ltr">My apologies. I've reported it now.<br>
</p>
<div class="gmail_quote">On 12 Feb 2015 21:47, "Teodoro Laino" <<a href="mailto:teodor...@gmail.com">teodor...@gmail.com</a>> wrote:<br type="attribution"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word">Which tone? If you believe that you have a problem with psfgen you should report this to the psfgen mailing list.<div><br><div><blockquote type="cite"><div>On 12 Feb 2015, at 15:07, Christian Jorgensen <<a href="mailto:chri...@gmail.com" target="_blank">chri...@gmail.com</a>> wrote:</div><br><div><div dir="ltr">Sorry I do not understand why the tone on<div>this board is like this. I'm simply asking for help.</div><div><br></div><div><br></div><div><br></div><div><br></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Thu, Feb 12, 2015 at 7:16 AM, Teodoro Laino <span dir="ltr"><<a href="mailto:teodor...@gmail.com" target="_blank">teodor...@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word">report this to the proper mailing list.<div><div><div><br><div><blockquote type="cite"><div>On 11 Feb 2015, at 23:04, Christian Jorgensen <<a href="mailto:chri...@gmail.com" target="_blank">chri...@gmail.com</a>> wrote:</div><br><div><div dir="ltr" style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px"><div>ATOM  49880  SOD SOD I  37      21.151   0.526 -30.628  1.00  0.00      ION NA</div><div>ATOM  49881  SOD SOD I  38      24.667 -35.051  19.114  1.00  0.00      ION NA</div><div>ATOM  49882  SOD SOD I  39     -12.620   2.426  26.969  1.00  0.00      ION NA</div><div>ATOM  49883  SOD SOD I  40     -10.705 -33.380 -11.158  1.00  0.00      ION NA</div><div>ATOM  49884  SOD SOD I  41     -19.491  29.350 -34.679  1.00  0.00      ION NA</div><div>ATOM  49885  SOD SOD I  42      40.802 -30.866  10.911  1.00  0.00      ION NA</div><div>ATOM  49886  SOD SOD I  43     -21.411 -20.389  17.270  1.00  0.00      ION NA</div><div>ATOM  49887  SOD SOD I  44      13.100  24.287  18.857  1.00  0.00      ION NA</div><div>ATOM  49888  SOD SOD I  45      33.628  30.716  18.333  1.00  0.00      ION NA</div><div>ATOM  49889  SOD SOD I  46      14.256 -31.556  -9.097  1.00  0.00      ION NA</div><div>ATOM  49890  SOD SOD I  47      -1.600  38.825  28.079  1.00  0.00      ION NA</div><div>ATOM  49891  SOD SOD I  48      26.911  -9.319  19.217  1.00  0.00      ION NA</div><div>ATOM  49892  CLA CLA I  49     -21.849 -29.233  -4.389  1.00  0.00      ION CL</div><div>ATOM  49893  CLA CLA I  50     -27.778  19.207  -8.907  1.00  0.00      ION CL</div><div>ATOM  49894  CLA CLA I  51      -1.036 -18.525 -33.557  1.00  0.00      ION CL</div><div>ATOM  49895  CLA CLA I  52     -37.955  23.751  -9.529  1.00  0.00      ION CL</div><div>ATOM  49896  CLA CLA I  53     -15.636 -34.005  12.873  1.00  0.00      ION CL</div><div>ATOM  49897  CLA CLA I  54      40.122  21.296 -26.349  1.00  0.00      ION CL</div><div>ATOM  49898  CLA CLA I  55      32.593  -9.101  17.836  1.00  0.00      ION CL</div><div>ATOM  49899  CLA CLA I  56       8.168 -24.215   8.246  1.00  0.00      ION CL</div><div>ATOM  49900  CLA CLA I  57      -4.530 -32.691  -6.031  1.00  0.00      ION CL</div><div>ATOM  49901  CLA CLA I  58     -14.998  37.422   2.603  1.00  0.00      ION CL</div><div>ATOM  49902  CLA CLA I  59     -22.559 -24.866 -37.160  1.00  0.00      ION CL</div><div>ATOM  49903  CLA CLA I  60      22.442 -17.653 -37.184  1.00  0.00      ION CL</div><div>ATOM  49904  CLA CLA I  61     -31.657   0.756 -22.411  1.00  0.00      ION CL</div><div>ATOM  49905  CLA CLA I  62     -25.707   4.569  26.200  1.00  0.00      ION CL</div><div>ATOM  49906  CLA CLA I  63       9.816  21.844 -29.523  1.00  0.00      ION CL</div><div>ATOM  49907  CLA CLA I  64      20.348  15.655  31.373  1.00  0.00      ION CL</div><div>ATOM  49908  CLA CLA I  65     -33.471  28.927  25.816  1.00  0.00      ION CL</div><div>ATOM  49909  CLA CLA I  66     -23.076 -36.320 -14.581  1.00  0.00      ION CL</div><div>ATOM  49910  CLA CLA I  67      11.228  23.055  26.442  1.00  0.00      ION CL</div><div>ATOM  49911  CLA CLA I  68     -31.967 -25.220  12.122  1.00  0.00      ION CL</div><div>ATOM  49912  CLA CLA I  69       7.122 -32.163 -23.902  1.00  0.00      ION CL</div><div>ATOM  49913  CLA CLA I  70     -30.542 -17.921  15.502  1.00  0.00      ION CL</div><div>ATOM  49914  CLA CLA I  71     -35.163 -32.044  11.857  1.00  0.00      ION CL</div><div>ATOM  49915  CLA CLA I  72      -1.340 -18.251 -21.790  1.00  0.00      ION CL</div><div><br></div><div><br></div><div>In relation to the error</div><div><br></div><div><br></div><div><div style="font-size:13px"><div>       49892           0</div><div> Two molecules have been defined as identical molecules but atoms mismatch charges!!</div><div>       49893           0</div><div> Two molecules have been defined as identical molecules but atoms mismatch charges!!</div><div>       49894           0</div><div> Two molecules have been defined as identical molecules but atoms mismatch charges!!</div><div>       49895           0</div><div> Two molecules have been defined as identical molecules but atoms mismatch charges!!</div><div>       49896           0</div><div> Two molecules have been defined as identical molecules but atoms mismatch charges!!</div><div>       49897           0</div><div> Two molecules have been defined as identical molecules but atoms mismatch charges!!</div></div><div style="font-size:13px">"</div></div><div><br></div><div><br></div><div>How can this be? I've generated this with the standard PSFGEN / Ionize plugin written</div><div>for VMD. </div><div><br></div><div><br></div><div><br></div><div><br></div><div><br></div><div><br></div><div><br></div></div><div class="gmail_extra" style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px"><br><div class="gmail_quote">On Wed, Feb 11, 2015 at 9:14 PM, Christian Jorgensen<span> </span><span dir="ltr"><<a href="mailto:chri...@gmail.com" target="_blank">chri...@gmail.com</a>></span><span> </span>wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><p dir="ltr">Hello Dr Laino</p><p dir="ltr">This is a problem with the ions. The atom indices it is warning about are all chlorine added to achieve electrical neutrality ( in VMD with Psfgen for NAMD)</p><p dir="ltr">I do not understand because I've used the standard procedure from Psfgen</p><div><div><div class="gmail_quote">On 11 Feb 2015 20:57, "Teodoro Laino" <<a href="mailto:teodor...@gmail.com" target="_blank">teodor...@gmail.com</a>> wrote:<br type="attribution"><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><div style="word-wrap:break-word">double check your PSF or PDB.. the error is self-esplicative : there must be two or more molecules that have the same name but have different atom sequence..<div><br></div><div>the fact your PSF or PDB may work with other codes means only that such codes are not performing tight checks.</div><div><br></div><div>Teo</div><div><br><div><blockquote type="cite"><div>On 11 Feb 2015, at 18:51, cjor <<a href="mailto:chri...@gmail.com" target="_blank">chri...@gmail.com</a>> wrote:</div><br><div><div dir="ltr">Hello, <div>I'm trying to run a QMMM simulation with CP2K based on a CHARMM FF MD simulation.</div><div><br></div><div>I first tried to run MM to see it works, but I get the following error:</div><div><br></div><div><br></div><div>"</div><div><div> CP2K| version string:                                          CP2K version 2.3</div><div> CP2K| source code revision number:                                        12343</div><div> CP2K| is freely available from                            <span> </span><a href="http://www.cp2k.org/" target="_blank">http://www.cp2k.org/</a></div><div> CP2K| Program compiled at                          Thu Feb 28 16:12:09 GMT 2013</div><div> CP2K| Program compiled on                                                popoca</div><div> CP2K| Program compiled for                                Linux-x86-64-gfortran</div><div> CP2K| Input file name                                                    mm.inp</div><div><br></div><div> GLOBAL| Force Environment number                                              1</div><div> GLOBAL| Basis set file name                                           BASIS_SET</div><div> GLOBAL| Geminal file name                                         BASIS_GEMINAL</div><div> GLOBAL| Potential file name                                           POTENTIAL</div><div> GLOBAL| MM Potential file name                                     MM_POTENTIAL</div><div> GLOBAL| Coordinate file name                                        ionized.pdb</div><div> GLOBAL| Method name                                                        CP2K</div><div> GLOBAL| Project name                                                    phd2_md</div><div> GLOBAL| Preferred FFT library                                             FFTSG</div><div> GLOBAL| Run type                                                             MD</div><div> GLOBAL| All-to-all communication in single precision                          F</div><div> GLOBAL| FFTs using library dependent lengths                                  F</div><div> GLOBAL| Global print level                                                  LOW</div><div> GLOBAL| Total number of message passing processes                             1</div><div> GLOBAL| Number of threads for this process                                    1</div><div> GLOBAL| This output is from process                                           0</div><div><br></div><div> MEMORY| system memory details [Kb]</div><div> MEMORY|                        rank 0           min           max       average</div><div> MEMORY| MemTotal            132089732     132089732     132089732     132089732</div><div> MEMORY| MemFree               2537384       2537384       2537384       2537384</div><div> MEMORY| Buffers                407408        407408        407408        407408</div><div> MEMORY| Cached               34948436      34948436      34948436      34948436</div><div> MEMORY| Slab                   732060        732060        732060        732060</div><div> MEMORY| SReclaimable           581768        581768        581768        581768</div><div> MEMORY| MemLikelyFree        38474996      38474996      38474996      38474996</div><div><br></div><div>       49892           0</div><div> Two molecules have been defined as identical molecules but atoms mismatch charges!!</div><div>       49893           0</div><div> Two molecules have been defined as identical molecules but atoms mismatch charges!!</div><div>       49894           0</div><div> Two molecules have been defined as identical molecules but atoms mismatch charges!!</div><div>       49895           0</div><div> Two molecules have been defined as identical molecules but atoms mismatch charges!!</div><div>       49896           0</div><div> Two molecules have been defined as identical molecules but atoms mismatch charges!!</div><div>       49897           0</div><div> Two molecules have been defined as identical molecules but atoms mismatch charges!!</div></div><div>"</div><div><br></div><div><br></div><div><br></div><div><br></div><div>I'm calling a PSF and PDF file that I know works. The error lies with the parsing of the </div><div>ion section (SOD and CLA).</div><div><br></div><div><br></div><div><br></div><div><br></div><div>My MM input is:</div><div><br></div><div><div>&GLOBAL</div><div> <span> </span>PRINT_LEVEL LOW</div><div> <span> </span>PREFERRED_FFT_LIBRARY  FFTSG</div><div> <span> </span>PROJECT phd2_md</div><div> <span> </span>RUN_TYPE MD</div><div>&END GLOBAL</div><div><br></div><div>&MOTION</div><div> <span> </span>&MD</div><div>   <span> </span>ENSEMBLE   NPT_I</div><div>   <span> </span>STEPS      6000</div><div>   <span> </span>TIMESTEP   0.48</div><div>   <span> </span>TEMPERATURE 298.0</div><div>   <span> </span>&THERMOSTAT</div><div>     <span> </span>TYPE NOSE</div><div>     <span> </span>REGION MASSIVE</div><div>     <span> </span>&NOSE</div><div>       <span> </span>TIMECON   [wavenumber_t] 1000</div><div>     <span> </span>&END NOSE</div><div>   <span> </span>&END THERMOSTAT</div><div>   <span> </span>&PRINT</div><div>     <span> </span>&ENERGY</div><div>       <span> </span>FILENAME =phd2_md.ener</div><div>       <span> </span>&EACH</div><div>         <span> </span>MD 1</div><div>       <span> </span>&END EACH</div><div>     <span> </span>&END ENERGY</div><div>     <span> </span>&PROGRAM_RUN_INFO</div><div>       <span> </span>&EACH</div><div>         <span> </span>MD 1</div><div>       <span> </span>&END EACH</div><div>     <span> </span>&END PROGRAM_RUN_INFO</div><div>   <span> </span>&END PRINT</div><div> <span> </span>&END MD</div><div> <span> </span>&PRINT</div><div>   <span> </span>&TRAJECTORY</div><div>     <span> </span>FILENAME =phd2_md.xyz</div><div>       <span> </span>&EACH</div><div>         <span> </span>MD 1</div><div>       <span> </span>&END EACH</div><div>   <span> </span>&END TRAJECTORY</div><div>   <span> </span>&RESTART</div><div>     <span> </span>FILENAME =phd2_md.restart</div><div>     <span> </span>BACKUP_COPIES 1</div><div>     <span> </span>&EACH</div><div>       <span> </span>MD 10</div><div>     <span> </span>&END EACH</div><div>   <span> </span>&END RESTART</div><div>   <span> </span>&RESTART_HISTORY OFF</div><div>   <span> </span>&END RESTART_HISTORY</div><div> <span> </span>&END PRINT</div><div>&END MOTION</div><div><br></div><div>&FORCE_EVAL</div><div> <span> </span>METHOD FIST                                   ! Using Molecular Mechanics</div><div> <span> </span>&MM</div><div>   <span> </span>&FORCEFIELD</div><div>     <span> </span>parm_file_name par_all27_prot_lipid.inp</div><div>     <span> </span>parmtype CHM</div><div>     <span> </span>ei_scale14 1.0</div><div>     <span> </span>vdw_scale14 1.0</div><div>     <span> </span>&SPLINE</div><div>       <span> </span>emax_spline 1.0</div><div>       <span> </span>rcut_nb 12</div><div>     <span> </span>&END SPLINE</div><div>   <span> </span>&END FORCEFIELD</div><div>   <span> </span>&POISSON</div><div>     <span> </span>&EWALD</div><div>       <span> </span>ewald_type SPME</div><div>       <span> </span>alpha 0.44</div><div>       <span> </span>gmax 81</div><div>     <span> </span>&END EWALD</div><div>   <span> </span>&END POISSON</div><div> <span> </span>&END MM</div><div><br></div><div> <span> </span>&SUBSYS</div><div>   <span> </span>&CELL</div><div>     <span> </span>abc 80 80 80</div><div>     <span> </span>periodic xyz</div><div>   <span> </span>&END CELL</div><div>   <span> </span>&KIND H</div><div>     <span> </span>BASIS_SET DZVP-GTH-BLYP</div><div>     <span> </span>POTENTIAL GTH-BLYP-q1</div><div>   <span> </span>&END KIND</div><div>   <span> </span>&KIND O</div><div>     <span> </span>BASIS_SET DZVP-GTH-BLYP</div><div>     <span> </span>POTENTIAL GTH-BLYP-q6</div><div>   <span> </span>&END KIND</div><div>   <span> </span>&KIND N</div><div>     <span> </span>BASIS_SET DZVP-GTH-BLYP</div><div>     <span> </span>POTENTIAL GTH-BLYP-q5</div><div>   <span> </span>&END KIND</div><div>   <span> </span>&KIND C</div><div>     <span> </span>BASIS_SET DZVP-GTH-BLYP</div><div>     <span> </span>POTENTIAL GTH-BLYP-q4</div><div>   <span> </span>&END KIND</div><div>   <span> </span>&KIND Fe2</div><div>     <span> </span>BASIS_SET DZVP-MOLOPT-SR-GTH</div><div>     <span> </span>POTENTIAL DZVP-MOLOPT-SR-GTH</div><div>   <span> </span>&END KIND</div><div><br></div><div>   <span> </span>&TOPOLOGY</div><div>     <span> </span>CONNECTIVITY    UPSF</div><div>     <span> </span>COORDINATE      PDB</div><div>     <span> </span>COORD_FILE_NAME     ionized.pdb</div><div>     <span> </span>CONN_FILE_NAME      ionized.psf</div><div>   <span> </span>&END TOPOLOGY</div><div> <span> </span>&END SUBSYS</div><div>&END FORCE_EVAL</div></div><div><br></div><div><br></div><div><br></div><div><br></div><div><br></div><div><br></div></div><div><br></div>--<span> </span><br>You received this message because you are subscribed to the Google Groups "cp2k" group.<br>To unsubscribe from this group and stop receiving emails from it, send an email to<span> </span><a href="mailto:cp2k+uns...@googlegroups.com" target="_blank">cp2k+uns...@googlegroups.com</a>.<br>To post to this group, send email to<span> </span><a href="mailto:cp...@googlegroups.com" target="_blank">cp...@googlegroups.com</a>.<br>Visit this group at<span> </span><a href="http://groups.google.com/group/cp2k" target="_blank">http://groups.google.com/group/cp2k</a>.<br>For more options, visit<span> </span><a href="https://groups.google.com/d/optout" target="_blank">https://groups.google.com/d/optout</a>.<br></div></blockquote></div><br></div></div><div><br></div>--<span> </span><br>You received this message because you are subscribed to a topic in the Google Groups "cp2k" group.<br>To unsubscribe from this topic, visit<span> </span><a href="https://groups.google.com/d/topic/cp2k/kkfMLpVx2Xo/unsubscribe" target="_blank">https://groups.google.com/d/topic/cp2k/kkfMLpVx2Xo/unsubscribe</a>.<br>To unsubscribe from this group and all its topics, send an email to<span> </span><a href="mailto:cp2k+uns...@googlegroups.com" target="_blank">cp2k+uns...@googlegroups.com</a>.<br>To post to this group, send email to<span> </span><a href="mailto:cp...@googlegroups.com" target="_blank">cp...@googlegroups.com</a>.<br>Visit this group at<span> </span><a href="http://groups.google.com/group/cp2k" target="_blank">http://groups.google.com/group/cp2k</a>.<br>For more options, visit<span> </span><a href="https://groups.google.com/d/optout" target="_blank">https://groups.google.com/d/optout</a>.<br></blockquote></div></div></div></blockquote></div><br><br clear="all"><div><br></div>--<span> </span><br><div><div dir="ltr"><div>_______</div><div><br></div>Christian Jørgensen</div></div></div><div style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px"><br></div><span style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;float:none;display:inline!important">--<span> </span></span><br style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px"><span style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;float:none;display:inline!important">You received this message because you are subscribed to the Google Groups "cp2k" group.</span><br style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px"><s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