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-us...@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 >> > _______________________________________________ > gmx-users mailing list gmx-us...@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 > > -- > 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/ =================================== _______________________________________________ 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
