[gmx-users] Temperature in Brownian Dynamics simulation

[Suman Chakrabarty]

Thanks Justin. I must have been too quick in my search and overlooked.
I shall try sd and find out if the problem gets resolved.


Regards,
Suman.


On Sat, Apr 18, 2009 at 5:28 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
> 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.