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</o:shapelayout></xml><![endif]--></head><body lang=EN-US link=blue vlink=purple><div class=WordSection1><p class=MsoNormal><span style='font-weight:normal'>Dear gromacs users,<o:p></o:p></span></p><p class=MsoNormal><span style='font-weight:normal'><o:p> </o:p></span></p><p class=MsoNormal><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. <o:p></o:p></span></p><p class=MsoNormal><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.<o:p></o:p></span></p><p class=MsoNormal><span style='font-weight:normal'>I have noticed that this issue has been already addressed:<o:p></o:p></span></p><p class=MsoNormal><span style='font-weight:normal'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-weight:normal'><a href="http://oldwww.gromacs.org/pipermail/gmx-users/2009-May/041836.html">http://oldwww.gromacs.org/pipermail/gmx-users/2009-May/041836.html</a><o:p></o:p></span></p><p class=MsoNormal><span style='font-weight:normal'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-weight:normal'>So I tried to switch from md (leap-frog) to md-vv integrator, but then temperature went up enormously <o:p></o:p></span></p><p class=MsoNormal><span style='font-weight:normal'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-weight:normal'>According to <o:p></o:p></span></p><p class=MsoNormal><span style='font-weight:normal'><a href="http://www.mail-archive.com/gmx-users@gromacs.org/msg32395.html">http://www.mail-archive.com/gmx-users@gromacs.org/msg32395.html</a><o:p></o:p></span></p><p class=MsoNormal><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?<o:p></o:p></span></p><p class=MsoNormal><span style='font-weight:normal'><o:p> </o:p></span></p><p class=MsoNormal><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? <o:p></o:p></span></p><p class=MsoNormal><span style='font-weight:normal'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-weight:normal'>My .mdp file is shown below.<o:p></o:p></span></p><p class=MsoNormal><span style='font-weight:normal'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-weight:normal'>Thank you very much in advance.<o:p></o:p></span></p><p class=MsoNormal><span style='font-weight:normal'>Mikhail<o:p></o:p></span></p><p class=MsoNormal><span style='font-weight:normal'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-weight:normal'>===============================<o:p></o:p></span></p><p class=MsoNormal><span style='font-weight:normal'>integrator = md or md-vv<o:p></o:p></span></p><p class=MsoNormal><span style='font-weight:normal'>dt = 0.001 ; time step<o:p></o:p></span></p><p class=MsoNormal><span style='font-weight:normal'>nsteps = 20000000 ; number of steps<o:p></o:p></span></p><p class=MsoNormal><span style='font-weight:normal'>comm_mode = Linear;Angular ; Remove center of mass translation and rotation<o:p></o:p></span></p><p class=MsoNormal><span style='font-weight:normal'>nstcomm = 1003 ; reset c.o.m. motion<o:p></o:p></span></p><p class=MsoNormal><span style='font-weight:normal'>nstxout = 10000 ; write coords<o:p></o:p></span></p><p class=MsoNormal><span style='font-weight:normal'>nstvout = 10000 ; write velocities<o:p></o:p></span></p><p class=MsoNormal><span style='font-weight:normal'>nstxtcout = 1000 ; write coords to xtc-trajectory file<o:p></o:p></span></p><p class=MsoNormal><span style='font-weight:normal'>nstlog = 1000 ; print to logfile<o:p></o:p></span></p><p class=MsoNormal><span style='font-weight:normal'>nstlist = 20 ; update pairlist<o:p></o:p></span></p><p class=MsoNormal><span style='font-weight:normal'>ns_type = grid ;simple ; pairlist method<o:p></o:p></span></p><p class=MsoNormal><span style='font-weight:normal'>;================== Polarizable model parameters =======================<o:p></o:p></span></p><p class=MsoNormal><span style='font-weight:normal'>emtol = 0.001 ;the convergency criterion for maximum force<o:p></o:p></span></p><p class=MsoNormal><span style='font-weight:normal'>niter = 50 ;maximum number of iterations for the shell particle optimization<o:p></o:p></span></p><p class=MsoNormal><span style='font-weight:normal'>;================= SHAKE/SETTLE Specification ===============================<o:p></o:p></span></p><p class=MsoNormal><span style='font-weight:normal'>shake_tol = 0.00001<o:p></o:p></span></p><p class=MsoNormal><span style='font-weight:normal'>;================= Cutt off specification =============================<o:p></o:p></span></p><p class=MsoNormal><span style='font-weight:normal'>pbc = xyz ; periodic boundary conditions<o:p></o:p></span></p><p class=MsoNormal><span style='font-weight:normal'>optimize_fft = yes ; perform FFT optimization at start<o:p></o:p></span></p><p class=MsoNormal><span style='font-weight:normal'>coulombtype = PME<o:p></o:p></span></p><p class=MsoNormal><span style='font-weight:normal'>ewald_geometry = 3dc<o:p></o:p></span></p><p class=MsoNormal><span style='font-weight:normal'>rcoulomb = 1.5 ;1.5 ; cut-off for coulomb<o:p></o:p></span></p><p class=MsoNormal><span style='font-weight:normal'>rlist = 1.5 ;1.5 ; cut-off for ns<o:p></o:p></span></p><p class=MsoNormal><span style='font-weight:normal'>vdw-type = cut-off<o:p></o:p></span></p><p class=MsoNormal><span style='font-weight:normal'>rvdw = 1.5 ;1.5 ; cut-off for vdw<o:p></o:p></span></p><p class=MsoNormal><span style='font-weight:normal'>dispcorr = EnerPres<o:p></o:p></span></p><p class=MsoNormal><span style='font-weight:normal'>;=======================================================================<o:p></o:p></span></p><p class=MsoNormal><span style='font-weight:normal'>Tcoupl = v-rescale ; ; temperature coupling<o:p></o:p></span></p><p class=MsoNormal><span style='font-weight:normal'>tc-grps = System<o:p></o:p></span></p><p class=MsoNormal><span style='font-weight:normal'>ref_t = 298.15<o:p></o:p></span></p><p class=MsoNormal><span style='font-weight:normal'>tau_t = 0.1<o:p></o:p></span></p><p class=MsoNormal><span style='font-weight:normal'>Pcoupl = no<o:p></o:p></span></p><p class=MsoNormal><span style='font-weight:normal'>;=======================================================================<o:p></o:p></span></p><p class=MsoNormal><span style='font-weight:normal'>gen_vel = no ; generate initial velocities<o:p></o:p></span></p><p class=MsoNormal><span style='font-weight:normal'>gen_temp = 300 ; initial temperature<o:p></o:p></span></p><p class=MsoNormal><span style='font-weight:normal'>gen_seed = -1 ; random seed<o:p></o:p></span></p><p class=MsoNormal><span style='font-weight:normal'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-weight:normal'>===============================================<o:p></o:p></span></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal><o:p> </o:p></p></div></body></html>