[gmx-users] Temperature in Brownian Dynamics simulation

[Justin A. Lemkul]

The issue you are reporting has already been discussed (hint: search the archives).

http://www.gromacs.org/pipermail/gmx-users/2007-July/028379.html

-Justin

Suman Chakrabarty wrote:
> Dear developers,
> 
> 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.
> 
> 
> Thanks,
> Suman.
> 
> 
> 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:
>>>> 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"
>>
>> 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
>> simulations?
>>
>>
>> Regards,
>> Suman.
>>
>>
>>>> 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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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================