Dear gromacs users, 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. 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. I have noticed that this issue has been already addressed:
http://oldwww.gromacs.org/pipermail/gmx-users/2009-May/041836.html So I tried to switch from md (leap-frog) to md-vv integrator, but then temperature went up enormously According to http://www.mail-archive.com/gmx-users@gromacs.org/msg32395.html this issue seems also be know , but I have not found if it was fixed in 4.5.x version? 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? My .mdp file is shown below. Thank you very much in advance. Mikhail =============================== integrator = md or md-vv dt = 0.001 ; time step nsteps = 20000000 ; number of steps comm_mode = Linear;Angular ; Remove center of mass translation and rotation nstcomm = 1003 ; reset c.o.m. motion nstxout = 10000 ; write coords nstvout = 10000 ; write velocities nstxtcout = 1000 ; write coords to xtc-trajectory file nstlog = 1000 ; print to logfile nstlist = 20 ; update pairlist ns_type = grid ;simple ; pairlist method ;================== Polarizable model parameters ======================= emtol = 0.001 ;the convergency criterion for maximum force niter = 50 ;maximum number of iterations for the shell particle optimization ;================= SHAKE/SETTLE Specification =============================== shake_tol = 0.00001 ;================= Cutt off specification ============================= pbc = xyz ; periodic boundary conditions optimize_fft = yes ; perform FFT optimization at start coulombtype = PME ewald_geometry = 3dc rcoulomb = 1.5 ;1.5 ; cut-off for coulomb rlist = 1.5 ;1.5 ; cut-off for ns vdw-type = cut-off rvdw = 1.5 ;1.5 ; cut-off for vdw dispcorr = EnerPres ;======================================================================= Tcoupl = v-rescale ; ; temperature coupling tc-grps = System ref_t = 298.15 tau_t = 0.1 Pcoupl = no ;======================================================================= gen_vel = no ; generate initial velocities gen_temp = 300 ; initial temperature gen_seed = -1 ; random seed ===============================================
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