[gmx-users] Temperature in Brownian Dynamics simulation

[Suman Chakrabarty]

Hi,

it was pointed out before that for Brownian Dynamics simulation, the
temperature calculated by g_energy does not match with the ref_t in
parameter file and it is almost double:
http://www.gromacs.org/pipermail/gmx-users/2007-June/028321.html ...
but unfortunately I find no follow-up to that post.

So I want to ask the question again here. I am doing Brownian Dynamics
simulation of a single polymer chain consisting of 100 atoms. While I
have set 300K as my simulation temperature, when I try to use g_energy
to check the temperature it reports the following:

Energy                      Average       RMSD     Fluct.      Drift  Tot-Drift
-------------------------------------------------------------------------------
Temperature                 624.188    44.0862    44.0862 -1.52693e-06
 -0.152693
T-Protein                   624.188    44.0862    44.0862 -1.52693e-06
 -0.152693


Here is the content of my mdp file:
=============================================================================
integrator          =  bd
dt                  =  0.002    ; ps !
nsteps              =  50000000 ; total 100 ns.

nstxout             =  1000
nstvout             =  0
nstfout             =  0
nstlist             =  10
nstlog              =  100

rlist               =  1.0
rvdw                =  1.0

bd_fric             =  0
ld_seed             =  -1

constraints         = all-bonds
lincs_order         = 8
lincs_iter          = 8

Tcoupl              =  no
tau_t               =  0.01
tc-grps             =  Protein
ref_t               =  300

Pcoupl              =  no

gen_vel             =  yes
gen_temp            =  300
gen_seed            =  173529
=============================================

Please help me troubleshoot this problem. Thanks.


Best regards,
Suman Chakrabarty.