[gmx-users] Temperature in Brownian Dynamics simulation
suman at sscu.iisc.ernet.in
Sat Apr 18 13:07:09 CEST 2009
could any of you please confirm whether one has to use certain general
thermostat in brownian dynamics (or stochastic dynamics) simulation or
"tcoupl = no" is justified? The manual says for stochastic dynamics
"the parameter tcoupl is ignored" (manual for ver. 4, page 141,
section 7.3.3). I would guess the same would be true for bd as well.
If "tcoupl = no" should be alright, then why the temperature obtained
from g_energy is almost double of the ref_t parameter? I have checked
this for a system consisting of a single polymer chain in vacuum.
If one has to use a general thermostat indeed, then please advise
which thermostat would be best appropriate for BD/SD simulations.
On Fri, Apr 17, 2009 at 4:55 PM, Suman Chakrabarty
<suman at sscu.iisc.ernet.in> wrote:
> On Fri, Apr 17, 2009 at 5:32 AM, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
>> Suman Chakrabarty wrote:
>>> 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"
> Are you sure? The manual says for stochastic dynamics "the parameter
> tcoupl is ignored" (manual for ver. 4, page 141, section 7.3.3). I
> would guess the same would be true for bd as well. For both sd and bd
> there should be a different Langevin thermostat applicable, where the
> temperature will be incorporated through the Gaussian distributed
> random force term.
> So I shall still need further clarification regarding this. Do I
> really need to mention a general MD thermostat? Won't it be ignored as
> mentioned for sd? If not, which thermostat is best for doing bd
>>> when I try to use g_energy
>>> to check the temperature it reports the following:
>>> Energy Average RMSD Fluct. Drift
>>> Temperature 624.188 44.0862 44.0862 -1.52693e-06
>>> T-Protein 624.188 44.0862 44.0862 -1.52693e-06
>>> 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.
More information about the gromacs.org_gmx-users