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<DIV><FONT color=#000000 size=2 face=Arial>Dear Gromacs users,</FONT></DIV>
<DIV><FONT size=2 face=Arial></FONT> </DIV>
<DIV><FONT size=2 face=Arial>I ran a production MD simulation on a ligand in a water box. I used NVT with coloumb and vdw cut-offs and avoided using PME. I analyzed the .edr file using g_lie after the simulation was finished, I found that at all the time steps, the energy was 0 KJ/mol, is that normal? How come the energy of the system is 0? </FONT></DIV>
<DIV><FONT size=2 face=Arial>'</FONT></DIV>
<DIV><FONT size=2 face=Arial>I am including both the simulation mdp file and the output of g_lie for inspection...</FONT></DIV>
<DIV><FONT size=2 face=Arial></FONT> </DIV>
<DIV><FONT size=2 face=Arial>I would appreciate if I could get any feedback about the reasons for this problem. </FONT></DIV>
<DIV><FONT size=2 face=Arial>Regards</FONT></DIV>
<DIV><FONT size=2 face=Arial></FONT> </DIV>
<DIV><FONT size=2 face=Arial>Hassan Shallal</FONT></DIV>
<DIV><FONT size=2 face=Arial>University of the Pacific</FONT></DIV>
<DIV><FONT size=2 face=Arial>Stockton, CA 95211</FONT></DIV>
<DIV><FONT size=2 face=Arial></FONT> </DIV>
<DIV><FONT size=2 face=Arial>The mdb file:</FONT></DIV>
<DIV><FONT size=2 face=Arial></FONT> </DIV>
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<DIV><FONT size=2 face=Arial>;RUN CONTROL PARAMETERS =<BR>integrator = md ; production<BR>tinit = 0 ; starting time for your run (only makes sense for integrators md, sd and bd)<BR>dt = 0.002 ; ps !<BR>nsteps = 2500000 ; total 5 ns.<BR>nstcomm = 1 ; frequency for center of mass motion removal<BR>;OUTPUT FREQUENCY OPRIONS FOR COORDINATES, VELOCITIES, AND FORCES = (because this is equilibration, we don't want to waste hard disk storgae space)<BR>nstxout = 1000 ; frequency to write coordinates to output trajectory file, the last coordinates are always written<BR>nstvout = 1000 ; frequency to write velocities to output trajectory, the last velocities are always written<BR>nstfout = 0 ; frequency to write forces to output trajectory.<BR>;OUTPUT FREQUENCY OPRIONS FOR ENERGIES =<BR>nstlog = 2500 ; frequency to write energies to log file, the last energies are always written<BR>nstenergy = 1000 ; frequency to write energies to energy file, the last energies are always written<BR>;NEIGHBOR SEARCHING PARAMETERS =<BR>nstlist = 10 ; neighbor list update frequency<BR>ns_type = grid ; ns algorithm (simple or grid)<BR>pbc = xyz ; periodic boundary conditions (xyz or none)<BR>rlist = 1 ; cut-off distance of the short-range neighbor list (nm)<BR>domain-decomposition = no<BR>;OUTPUT FREQUENCY AND PRESISION FOR XTC FILES =<BR>nstxtcout = 5000 ; frequency to write coordinates to xtc trajectory (STEPS)<BR>xtc-precision = 1000 ; precision to write to xtc trajectory<BR>energygrps = SOL UNK <BR>;OPTIONS FOR ELECTROSTATIC AND VDW =<BR>coulombtype = Cut-off ; method of doing electrostatics (Twin range cut-off’s with neighborlist cut-off rlist and Coulomb cut-off rcoulomb,<BR>where rcoulomb ≥ rlist.)<BR>rcoulomb_switch = 0 ; where to start switching the Coulomb potential (nm)<BR>rcoulomb = 1 ; distance for Coulomb cut-off (nm)<BR>epsilon_r = 1 ; the relative dielectric constant (1 or zero, if zero, means infinity)<BR>vdwtype = Cut-off ; method of doing VDW (Twin range cut-off’s with neighbor list cut-off rlist and VdW cut-off rvdw, where<BR>rvdw ≥ rlist.)<BR>rvdw = 1 ; distance for LJ or Buckingham cut-off (nm)<BR>DispCorr = no ; Don't apply long range dispersion corrections for Energy and Pressure<BR>;OPTIONS FOR TEMPERATURE COUPLING = <BR>Tcoupl = v-rescale <BR>tau_t = 0.1 ; time constant for coupling in ps (one for each group in tc grps), 0 means no temperature coupling<BR>tc_grps = System ; to avoid hot solvent cold solute situation<BR>ref_t = 298.15 <BR>;OPTIONS FOR PRESSURE COUPLING<BR>Pcoupl = no<BR>pcoupltype = isotropic ; Isotropic pressure coupling with time constant<BR>tau_p = 0.5 ; time constant for coupling in ps<BR>compressibility = 4.5e-05 ; compressibility for water at 1 atm and 300 K<BR>ref_p = 1.0 </FONT></DIV>
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<DIV><FONT size=2 face=Arial>The .xvg g_lie output file:</FONT></DIV>
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<DIV># This file was created Fri May 21 17:21:18 2010<BR># by the following command:<BR># g_lie -f 4_pr_NVT.edr -o 4_pr_NVT.xvg <BR>#<BR># g_lie is part of G R O M A C S:<BR>#<BR># Grunge ROck MAChoS<BR>#<BR>@ title "LIE free energy estimate"<BR>@ xaxis label "Time (ps)"<BR>@ yaxis label "DGbind (kJ/mol)"<BR>@TYPE xy<BR> 0 0<BR> 2 0<BR> 4 0<BR> 6 0<BR> 8 0<BR> 10 0<BR> 12 0<BR> 14 0<BR> 16 0<BR> 18 0<BR> 20 0<BR> 22 0<BR>all the way until</DIV>
<DIV> 5000 0<BR> 0 0<BR>------------------------------------------------------------------------------------------------------------</DIV></FONT></DIV></BODY></HTML>