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 <jalem...@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 >> <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
