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 <su...@sscu.iisc.ernet.in> wrote: > On Fri, Apr 17, 2009 at 5:32 AM, Mark Abraham <mark.abra...@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@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
