Dear gmx-users, I have performed further investigation on the subject of the velocity distribution
http://lists.gromacs.org/pipermail/gmx-users/2011-April/060316.html and what I found looks like a sort of a bug to me. Namely, the velocity distribution profiles are different if I simulate a thermalized wall via dimmers with one on the particles being fixed: ==================================== [ moleculetype ] ; molname nrexcl ROCK 1 [ atoms ] ;id type resnr residu atom cgnr charge 1 PRC 1 ROCK PRC 1 0 2 FRC 1 ROCK FRC 2 0 [bonds] ; i j funct length force.c. 1 2 1 0.0 1000 ==================================== energygrps = FRC PRC tcoupl = v-rescale tc-grps = PRC FRC tau_t = 0.5 0 ref_t = 300 0 freezegrps = FRC freezedim = Y Y Y energygrp_excl = FRC FRC FRC PRC PRC PRC =================================== or using position_restraints approach: ==================================== [ moleculetype ] ; molname nrexcl ROCK 1 [ atoms ] ;id type resnr residu atom cgnr charge 1 PRC 1 ROCK PRC 1 0 [ position_restraints ] ; iatom type fx fy fz 1 1 10000 10000 10000 ================================== energygrps = PRC tcoupl = v-rescale tc-grps = PRC tau_t = 0.5 ref_t = 300 energygrp_excl = PRC PRC ============================== For both simulations I built the velocity distribution function using g_traj. In both cases the average kinetic temperature (I have calculated it from the averaged kinetic energy based on the velocity distributions) corresponds well to the one assigned to the thermostat (300 K). But, a) the velocity distributions for these two cases differ from each other; b) neither of them is Maxwellian. In my simulations I use 4.5.3 version of GROMACS. I am really lost and would very much appreciate any comments. Many thanks in advance. Mikhail.
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