ref_p = 0.0 0.0 ?? Are you sure about this??
On Tue, Jun 11, 2013 at 12:08 PM, Dr. Vitaly Chaban <vvcha...@gmail.com>wrote: > 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 > -- 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