[gmx-users] Temperature in Brownian Dynamics simulation

[Mark Abraham]

Suman Chakrabarty wrote:
> 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,

I don't think you have. You've generated velocities at that temperature, 
but you're not thermostatting to that temperature, since you have 
"Tcoupl = no"

Mark

> 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.
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