Dear list, I am trying to use MTTK barostat in GROMACS 4.5.5. After analyzing the result for a while, I found that the conserved energy (not total energy) of MTTK is drifting during the simulation. The .xvg, .edr files are uploaded at [1] and [2]. It is drifting with a constant ratio of ca. -185 kJ/mol/ps.
I cannot believe this is an expected behavior, so could anyone point out where I am wrong in my simulation setup? I found similar report at [3] but seems it was when 4.5 was in pre-release stage. Thanks in advance for your help! * Simulation detail The system consists of 1000 SPC-E water molecules, and the time step is set to 0.5 fs, just in case the long timestep harms the conserevation (c.f. [3]). The interaction energy is set to switching version, just in case, too. Changing these parameter does not seem to improve the conservation. The double precision version of GROMACS is used (single precision version also has the same problem). The system has been pre-equilibrated with Berendsen pressure coupling simulation with the same pressure and temperature. [1] https://www.dropbox.com/s/16bgfhvavqcw1f8/mttk05.xvg [2] https://www.dropbox.com/s/tg8butw39rmz8qk/mttk05.edr [3] http://lists.gromacs.org/pipermail/gmx-developers/2010-January/003979.html == .mdp file contents follow integrator = md-vv define = dt = 0.0005 nsteps = 1000000 ; 500 ps coulombtype = PME-Switch vdwtype = Switch pbc = xyz rlist = 1.2 rcoulomb = 1.0 rcoulomb_switch = 0.9 rvdw = 1.0 rvdw_switch = 0.9 nstlist = 1 tinit = 0 tcoupl = nose-hoover tc_grps = System tau_t = 0.5 ref_t = 300.0 nsttcouple = 1 pcoupl = MTTK pcoupltype = isotropic compressibility = 4.5e-5 ref_p = 1.01325 tau_p = 0.5 refcoord_scaling = no nstpcouple = 1 constraints = hbonds constraint_algorithm = LINCS nstxtcout = 100 nstlog = 100 nstenergy = 100 nstvout = 0 nstxout = 1000 -- Shun SAKURABA, Ph.D. Postdoc @ Molecular Modeling & Simulation Group, Japan Atomic Energy Agency -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
