[gmx-users] Membrane Equilibration
hanniballecter13 at gmail.com
Tue Jun 11 19:13:15 CEST 2013
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
> > 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
> > 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
> > 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.
> > --
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