[gmx-users] Temperature in Brownian Dynamics simulation

[Suman Chakrabarty]

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.
>> _______________________________________________
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before posting!
>> Please don't post (un)subscribe requests to the list. Use the www
>> interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
> --
> This message has been scanned for viruses and
> dangerous content by MailScanner, and is
> believed to be clean.
>
>



-- 
===================================
Suman Chakrabarty
SSCU (Room # 106A)
Indian Institute of Science,
Bangalore, India.
PIN: 560012
Mobile: +91 98800 87948
            +1 607 342 4366
Homepage: http://www.namusite.com/
===================================