Hello everybody, I am trying to simulate a triclinic cristal lattice (4x4x2) with gromacs (4.5.5) in constant pressure with the Parrinello-Rahman (PR) barostat. the crystal were previously equilibrated in the NPT ensemble during 1ns at 200K with berendsen thermostat/barostat . The crystal initail parameters are (28.736 32.292 34.142 91.04 93.50 110.06 P 1)
I used the following parameters ..... Tcoupl = v-rescale tc-grps = BCL BEN tau-t = 0.1 0.1 ref-t = 200 200 ; Pressure coupling is on Pcoupl = Parrinello-Rahman pcoupltype = isotropic tau_p = 5.0 compressibility = 4.5e-5 ref_p = 1.0135 gen_vel = no DispCorr = EnerPres ..... With these parameters, the system explodes. I am confused here because if I switch to the berendsen barostat with the following parameters I have no problems to do a simulation of 1ns and the crystal lattice parameters remains stable (see below) ..... isotropic Tcoupl = v-rescale tc-grps = BCL BEN tau-t = 0.1 0.1 ref-t = 200 200 ; Pressure coupling is on Pcoupl = berendsen pcoupltype = isotropic tau_p = 2.0 compressibility = 4.5e-5 ref_p = 1.0135 gen_vel = no DispCorr = EnerPres ..... Energy Average Err.Est. RMSD Tot-Drift ------------------------------------------------------------------------------- Temperature 199.576 0.023 3.56331 0.0876693 (K) Pressure 1.0242 0.25 971.331 -0.346972 (bar) Box-X 2.91464 5.7e-05 0.00129697 6.17829e-05 (nm) Box-Y 3.07662 6e-05 0.00136905 6.52159e-05 (nm) Box-Z 3.4535 6.7e-05 0.00153675 7.3165e-05 (nm) Volume 30.9685 0.0018 0.0413433 0.00197128 (nm^3) T-BCL 199.516 0.02 3.83149 0.0860062 (K) T-BEN 199.981 0.048 9.94395 0.0989034 (K) CRYST1 29.137 32.742 34.618 91.04 93.50 110.06 P 1 Did I miss something important here about PR and crystals? SA -- 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
