[gmx-users] Membrane Equilibration
jalemkul at vt.edu
Tue Jun 11 19:17:17 CEST 2013
On 6/11/13 1:13 PM, HANNIBAL LECTER wrote:
> ref_p = 0.0 0.0 ??
> Are you sure about this??
That's a likely culprit. See below for another.
> 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
>>> file obtained from that run to start a new run using Parrinello-Rahman. I
>>> 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
>>> 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
>>> 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
Here is another issue. You're re-generating velocities (destroying the previous
equilibration) with a barostat that doesn't usually play nice under such
circumstances, and you're generating velocities for a temperature well below the
target defined in ref_t. That can cause the thermostat to go haywire, which
then has negative effects on the pressure (which comes from kinetic energy and
the virial), which can lead to collapse.
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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