[gmx-users] Membrane Equilibration

[Dr. Vitaly Chaban]

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.
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