[gmx-users] Membrane Equilibration

[HANNIBAL LECTER]

ref_p                    = 0.0  0.0 ??

Are you sure about this??


On Tue, Jun 11, 2013 at 12:08 PM, Dr. Vitaly Chaban <vvchaban at 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 <nshafique at 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 at 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-request at gromacs.org.
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> --
> gmx-users mailing list    gmx-users at 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-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>