[gmx-users] Re: Membrane Equilibration

[Justin Lemkul]

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

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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