[gmx-users] Temperature in Brownian Dynamics simulation
suman at sscu.iisc.ernet.in
Fri Apr 17 13:25:38 CEST 2009
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.
>> gmx-users mailing list gmx-users at gromacs.org
>> 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
> 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.
SSCU (Room # 106A)
Indian Institute of Science,
Mobile: +91 98800 87948
+1 607 342 4366
More information about the gromacs.org_gmx-users