[gmx-users] Re: Membrane Equilibration
jalemkul at vt.edu
Tue Jun 11 19:31:49 CEST 2013
On 6/11/13 1:25 PM, Neha wrote:
> Hi everybody,
> Thank you so much for taking the time to read this.
> I thought ref_p would need to be 0.0 and 0.0 if I wanted zero surface
> tension. How else could I get a tensionless membrane?
As far as I understand, surface tension is only applied when using "pcoupl =
surface-tension" and then ref_p specifies the value of surface tension in
bar-nm. Normally, ref_p specifies the reference pressure for an NPT ensemble.
> As for the generating velocities, I completely forgot that would ruin the
> equilibrium. Would you recommend saying gen_vel = no or simply raising the
> gen_temp closer to the required value? If the second how close do you think
> I should keep it? Sorry for bombarding you guys with so many questions!
gen_temp is irrelevant when gen_vel is set to "no."
> Also no one has commented on this so I'm guessing using the structure file
> from the Berendsen run is an okay way to do what I want?
The configuration alone is insufficient. You should preserve the previous
ensemble by passing the final .cpt file to grompp -t.
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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