Hi, I was also facing the same problem. If you check your pressure during this NPT run, u can see that it got increased to a higher value. I had posted the same problem few days back, u can follow the thread. It seems MTTK is not stable enough and is not performing well in this context. So I have moved to Leap-frog, Nose-Hoover, Parinello-Rahman combination for the NPT simulation. There is one paper as well by Prof. Shirts in JCTC.
Cheers, Tarak On Thu, Nov 22, 2012 at 2:08 PM, Shun Sakuraba <sakuraba.s...@jaea.go.jp> wrote: > 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 -- 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
