<div dir="ltr"><div style>Hello Fahimeh,</div><div><br></div>Check the energy components: bonds, angles, torsion angles, coulomb and vdw. I believe the bonded interactions energies should agree perfectly, otherwise there is a mismatch between topologies and/or forcefield you use in gromacs and cp2k. If those are ok, then I guess this discrepancy is due to differences in PME electrostatics calculation/implementation.<div>
<br></div><div style>Regards,</div><div style>Peter</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Tue, Aug 6, 2013 at 8:00 PM, Fahimeh Baftizadeh <span dir="ltr"><<a href="mailto:fahimeh.b...@googlemail.com" target="_blank">fahimeh.b...@googlemail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hello everyone, <div><br></div><div>I thought maybe it will be helpful if I just put here my input files and someone else run it if it is possible for you. In fact it seems very trivial but I checked the parameters and I don't understand why the Energy is positive! </div>
<div><br></div><div>I am doing just a single step energy calculation of a molecule. </div><div>Thanks for your help</div><span class="HOEnZb"><font color="#888888"><div><br></div><div>Fahimeh</div></font></span><div class="HOEnZb">
<div class="h5"><div><br></div><div><br><br>On Monday, August 5, 2013 4:53:08 PM UTC-4, Fahimeh Baftizadeh wrote:<blockquote class="gmail_quote" style="margin:0;margin-left:0.8ex;border-left:1px #ccc solid;padding-left:1ex">
Hello,<div><br></div><div>I have a system which contains only one molecule in gas phase. I wanna compute its energy with cp2k and gromacs (for a test).</div><div>I am reading a pdb file and the force filed is in amber format, this is cp2k input file:</div>
<div><br></div><div><div>&FORCE_EVAL</div><div> METHOD FIST</div><div> &MM</div><div> &FORCEFIELD</div><div> &SPLINE</div><div> EMAX_ACCURACY 500.0</div><div> EMAX_SPLINE 1000.0</div>
<div> EPS_SPLINE [hartree] 1.00000000E-07</div><div> &END</div><div> parm_file_name /home/fbafti/work/nucleation/<u></u>test-ff/single-mol/amber-1res.<u></u>top</div><div> parmtype AMBER</div><div>
&END FORCEFIELD</div><div> &POISSON</div><div> &EWALD</div><div> EWALD_TYPE pme</div><div> RCUT [angstrom] 8.0</div><div> EPSILON 1E-6</div><div> &END EWALD</div><div> &END POISSON</div>
<div> &PRINT</div><div> &FF_INFO</div><div> &END</div><div> &END</div><div> &END MM</div><div> &SUBSYS</div><div> &CELL</div><div> ABC 125.990 122.910 129.640</div><div>
&END</div><div> &TOPOLOGY</div><div> COORD_FILE_NAME /home/fbafti/work/nucleation/<u></u>test-ff/single-mol/non-per.pdb</div><div> COORDINATE PDB</div><div> CONN_FILE_NAME /home/fbafti/work/nucleation/<u></u>test-ff/single-mol/amber-1res.<u></u>top</div>
<div> CONN_FILE_FORMAT AMBER</div><div> &END TOPOLOGY</div><div> &END SUBSYS</div><div> STRESS_TENSOR ANALYTICAL</div><div>&END FORCE_EVAL</div><div>&GLOBAL</div><div> PROJECT paracetamol_single_mol</div>
<div> RUN_TYPE ENERGY</div><div>&END GLOBAL</div></div><div><br></div><div><br></div><div>I put a very large box size, just to be sure that there are no periodic images in the energy estimation. The energy output of CP2K has a value which is larger than zero and it is strange.</div>
<div>I performed a single step steepest decent with gromacs and I got another value which is minus and makes more sense.</div><div>I already checked the electrostatic parameters and vdw ... I think they are all similar while the energy difference coming from gromacs and cp2k differs by almost 500 kj/mol and in gromacs is minus and in cp2k is a plus value.</div>
<div><br></div><div>This is the gromacs input file: </div><div><div><br></div><div>integrator = steep</div><div>comm_mode = Linear</div><div>dt = 0.001</div><div>nsteps = 1</div>
<div>; Output frequency for coords (x), velocities (v) and forces (f) =</div><div>nstxout = 1</div><div>nstvout = 1</div><div>; Output frequency for energies to log file and energy file =</div>
<div>nstlog = 1</div><div>nstenergy = 1</div><div>nstxtcout = 1</div><div>xtc-precision = 1000000</div><div>xtc_grps = System</div><div>energygrps = System</div>
<div>pbc = xyz</div><div>nstlist = 10</div><div>epsilon_r = 1.</div><div>ns_type = grid ; or grid I don't know</div><div>coulombtype = pme</div>
<div>vdwtype = Cut-off</div><div>fourierspacing = 0.12</div><div>; EWALD/PME/PPPM parameters</div><div>pme_order = 4</div><div>ewald_rtol = 1e-05</div><div>epsilon_surface = 0</div>
<div>optimize_fft = yes</div><div>rlist = 0.8</div><div>rcoulomb = 0.8</div><div>rvdw = 0.8</div><div>emtol = 1.0</div></div><div><br></div>
<div>Can anybody help me with that?</div><div>Thanks</div><div>Fahimeh</div></blockquote></div>
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