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, 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
