what happens to your energy before the observed crash? does the crash happen at the same time-step each time?
Dr. Vitaly Chaban On Tue, Jun 11, 2013 at 5:22 PM, Neha <nshafi...@wesleyan.edu> wrote: > Hi everybody, > > I am trying to simulate a lipid bilayer and wanted to use Parrinello Rahman > coupling. However, I read that Parinello-Rahman is not great for > equilibration so I thought I would do a small run using the Berendsen > barostat to decrease the chances of large oscillations. I then used the > .gro > file obtained from that run to start a new run using Parrinello-Rahman. I > am > not sure if that's the correct way to go about doing what I want to do. > > My Parrinello run also terminated a little while in, with the error that 2 > of my atoms have moved further apart than the cut-off distance. A part of > my > mdp file is pasted below and I was wondering if anyone had any suggestions > as to stop that from happening. My time step is 0.02 ps and I thought > increasing tau-p might work. I am using the compressibility from the map > file on the Martini website and am worried that might be too large. Any > help > will be super useful! Let me know if you need any more information. > > > ; OPTIONS FOR WEAK COUPLING ALGORITHMS = > ; Temperature coupling = > tcoupl = nose-hoover > ; Groups to couple separately = > tc-grps = DPPC W > ; Time constant (ps) and reference temperature (K) = > tau_t = 1.0 1.0 > ref_t = 320 320 > nsttcouple = 1 > ; Pressure coupling = > Pcoupl = Parrinello-Rahman > Pcoupltype = semiisotropic > ; Time constant (ps), compressibility (1/bar) and reference P (bar) = > tau_p = 5.0 5.0 > compressibility = 3e-4 3e-4 > ref_p = 0.0 0.0 > nstpcouple = 5 > > ; GENERATE VELOCITIES FOR STARTUP RUN = > gen_vel = yes > gen_temp = 105 > gen_seed = 473529 > > > > -- > View this message in context: > http://gromacs.5086.x6.nabble.com/Membrane-Equilibration-tp5009038.html > Sent from the GROMACS Users Forum mailing list archive at Nabble.com. > -- > 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
