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Hi,<br><br>The integrator is not the issue. The cut-off setup is. <br>You should use interactions that go smoothly to zero with a buffer region in the neighborlist.<br>Use for instance shift for LJ interactions. PME could be switched, but that is a much smaller<br>contribution. Use rlist about 0.3 nm larger than rvdw (and rcoulomb if you switch PME).<br>Note that your current cut-off's are overly long.<br><br>All this probably doesn't matter much for the surface tension.<br><br>PS spatially isotropic dispersion correction does not work for the surface tension,<br>you need to determine the dispersion correction to the surface tension analytically.<br><br>Berk<br><br><hr id="stopSpelling">From: mstukan@slb.com<br>To: gmx-users@gromacs.org<br>Date: Wed, 1 Dec 2010 12:10:23 +0000<br>Subject: [gmx-users] v-rescale and conserved energy<br><br>
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</style><div class="ecxWordSection1"><p class="ecxMsoNormal"><span style="font-weight: normal;">Dear gromacs users,</span></p><p class="ecxMsoNormal"><span style="font-weight: normal;"> </span></p><p class="ecxMsoNormal"><span style="font-weight: normal;">I am running NVT simulations for polarizable (shell particle) water model (GROMACS version 4.5.1 and 4.5.3 (issue is same in both)) using v-rescale thermostat. </span></p><p class="ecxMsoNormal"><span style="font-weight: normal;">While temperature, potential, kinetic and total energies behave quite well I am failing to obtain constant values for Conserved-Energy. It drifts quite significantly: 1000 kJ/mol/ns with average value 32500 kJ/mol.</span></p><p class="ecxMsoNormal"><span style="font-weight: normal;">I have noticed that this issue has been already addressed:</span></p><p class="ecxMsoNormal"><span style="font-weight: normal;"> </span></p><p class="ecxMsoNormal"><span style="font-weight: normal;"><a href="http://oldwww.gromacs.org/pipermail/gmx-users/2009-May/041836.html" target="_blank">http://oldwww.gromacs.org/pipermail/gmx-users/2009-May/041836.html</a></span></p><p class="ecxMsoNormal"><span style="font-weight: normal;"> </span></p><p class="ecxMsoNormal"><span style="font-weight: normal;">So I tried to switch from md (leap-frog) to md-vv integrator, but then temperature went up enormously </span></p><p class="ecxMsoNormal"><span style="font-weight: normal;"> </span></p><p class="ecxMsoNormal"><span style="font-weight: normal;">According to </span></p><p class="ecxMsoNormal"><span style="font-weight: normal;"><a href="http://www.mail-archive.com/gmx-users@gromacs.org/msg32395.html" target="_blank">http://www.mail-archive.com/gmx-users@gromacs.org/msg32395.html</a></span></p><p class="ecxMsoNormal"><span style="font-weight: normal;">this issue seems also be know , but I have not found if it was fixed in 4.5.x version?</span></p><p class="ecxMsoNormal"><span style="font-weight: normal;"> </span></p><p class="ecxMsoNormal"><span style="font-weight: normal;">Am I doing something obviously wrong? And should Conserved-Energy drift be a real problem if the purpose of the simulation is calculation of the surface tension? </span></p><p class="ecxMsoNormal"><span style="font-weight: normal;"> </span></p><p class="ecxMsoNormal"><span style="font-weight: normal;">My .mdp file is shown below.</span></p><p class="ecxMsoNormal"><span style="font-weight: normal;"> </span></p><p class="ecxMsoNormal"><span style="font-weight: normal;">Thank you very much in advance.</span></p><p class="ecxMsoNormal"><span style="font-weight: normal;">Mikhail</span></p><p class="ecxMsoNormal"><span style="font-weight: normal;"> </span></p><p class="ecxMsoNormal"><span style="font-weight: normal;">===============================</span></p><p class="ecxMsoNormal"><span style="font-weight: normal;">integrator = md or md-vv</span></p><p class="ecxMsoNormal"><span style="font-weight: normal;">dt = 0.001 ; time step</span></p><p class="ecxMsoNormal"><span style="font-weight: normal;">nsteps = 20000000 ; number of steps</span></p><p class="ecxMsoNormal"><span style="font-weight: normal;">comm_mode = Linear;Angular ; Remove center of mass translation and rotation</span></p><p class="ecxMsoNormal"><span style="font-weight: normal;">nstcomm = 1003 ; reset c.o.m. motion</span></p><p class="ecxMsoNormal"><span style="font-weight: normal;">nstxout = 10000 ; write coords</span></p><p class="ecxMsoNormal"><span style="font-weight: normal;">nstvout = 10000 ; write velocities</span></p><p class="ecxMsoNormal"><span style="font-weight: normal;">nstxtcout = 1000 ; write coords to xtc-trajectory file</span></p><p class="ecxMsoNormal"><span style="font-weight: normal;">nstlog = 1000 ; print to logfile</span></p><p class="ecxMsoNormal"><span style="font-weight: normal;">nstlist = 20 ; update pairlist</span></p><p class="ecxMsoNormal"><span style="font-weight: normal;">ns_type = grid ;simple ; pairlist method</span></p><p class="ecxMsoNormal"><span style="font-weight: normal;">;================== Polarizable model parameters =======================</span></p><p class="ecxMsoNormal"><span style="font-weight: normal;">emtol = 0.001 ;the convergency criterion for maximum force</span></p><p class="ecxMsoNormal"><span style="font-weight: normal;">niter = 50 ;maximum number of iterations for the shell particle optimization</span></p><p class="ecxMsoNormal"><span style="font-weight: normal;">;================= SHAKE/SETTLE Specification ===============================</span></p><p class="ecxMsoNormal"><span style="font-weight: normal;">shake_tol = 0.00001</span></p><p class="ecxMsoNormal"><span style="font-weight: normal;">;================= Cutt off specification =============================</span></p><p class="ecxMsoNormal"><span style="font-weight: normal;">pbc = xyz ; periodic boundary conditions</span></p><p class="ecxMsoNormal"><span style="font-weight: normal;">optimize_fft = yes ; perform FFT optimization at start</span></p><p class="ecxMsoNormal"><span style="font-weight: normal;">coulombtype = PME</span></p><p class="ecxMsoNormal"><span style="font-weight: normal;">ewald_geometry = 3dc</span></p><p class="ecxMsoNormal"><span style="font-weight: normal;">rcoulomb = 1.5 ;1.5 ; cut-off for coulomb</span></p><p class="ecxMsoNormal"><span style="font-weight: normal;">rlist = 1.5 ;1.5 ; cut-off for ns</span></p><p class="ecxMsoNormal"><span style="font-weight: normal;">vdw-type = cut-off</span></p><p class="ecxMsoNormal"><span style="font-weight: normal;">rvdw = 1.5 ;1.5 ; cut-off for vdw</span></p><p class="ecxMsoNormal"><span style="font-weight: normal;">dispcorr = EnerPres</span></p><p class="ecxMsoNormal"><span style="font-weight: normal;">;=======================================================================</span></p><p class="ecxMsoNormal"><span style="font-weight: normal;">Tcoupl = v-rescale ; ; temperature coupling</span></p><p class="ecxMsoNormal"><span style="font-weight: normal;">tc-grps = System</span></p><p class="ecxMsoNormal"><span style="font-weight: normal;">ref_t = 298.15</span></p><p class="ecxMsoNormal"><span style="font-weight: normal;">tau_t = 0.1</span></p><p class="ecxMsoNormal"><span style="font-weight: normal;">Pcoupl = no</span></p><p class="ecxMsoNormal"><span style="font-weight: normal;">;=======================================================================</span></p><p class="ecxMsoNormal"><span style="font-weight: normal;">gen_vel = no ; generate initial velocities</span></p><p class="ecxMsoNormal"><span style="font-weight: normal;">gen_temp = 300 ; initial temperature</span></p><p class="ecxMsoNormal"><span style="font-weight: normal;">gen_seed = -1 ; random seed</span></p><p class="ecxMsoNormal"><span style="font-weight: normal;"> </span></p><p class="ecxMsoNormal"><span style="font-weight: normal;">===============================================</span></p><p class="ecxMsoNormal"> </p><p class="ecxMsoNormal"> </p><p class="ecxMsoNormal"> </p></div><br>--
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