[gmx-users] Velocity distribution

Mikhail Stukan mstukan at slb.com
Tue Apr 12 09:01:46 CEST 2011

Dear gmx-users,

I am currently trying to simulate a thermalized wall of coarse-grained particles. I model the wall in the framework of the bead on spring approach.  The wall molecules are defined as dimers :

[ 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

; i j funct length        force.c.
  1 2 1       0.0          1000

And then the beads of one type (FRC) are defined to be fixed and no thermostat is applied to them. There are no interactions between the particles in the system (ensemble of ideal harmonic oscillators):

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

The problem I have is that when I build the velocity distribution for the mobile particles (atom type PRC), the distribution does not correspond to the Maxwell's distribution (is shifted to the left). Am I missing something very basic? In my previous simulations for the same system but using another MD code with stochastic (DPD) thermostat the Maxwellian  distribution was reproduced without any problem.

Many thanks in advance,

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110412/877167f2/attachment.html>

More information about the gromacs.org_gmx-users mailing list