[gmx-users] Semiisotropic pressure coupling

[Justin Lemkul]

On 2/15/15 1:02 PM, shivangi nangia wrote:
> Dear Justin,
>
> Thanks for the continuous help.
>
> Since I have done reverse CG, The CG POPC was equilibrated alone
> anisotropically, The APL was fine there.
> On reverse CG and NVT its still fine, it only after NPT it starts dropping.
>

Of course it's fine during NVT - the box can't change so the area is constant.

> I am calculating APL as (2*Lx*Ly)/(No. of Lipids).
>

That's only valid for pure, symmetric membranes.  You have a protein embedded in 
one leaflet, so this method is wrong.

> You mentioned to get gull force field from your site, is it here:
>
> http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs
>

Yes, that's the right place.

> On unzipping this I see POPC is an .trp entry.
>
> If there is some other database, kindly point it out to me.
>

What I'm telling you is to use those force field files to (1) verify that your 
POPC parameters are right (they should be) and (2) you'll have the right protein 
topology (there are different bonded parameters that will affect protein dynamics).

Again, I must emphasize - troubleshooting the APL of this system with respect to 
the known APL of pure POPC is pointless.  You have a protein that convolutes 
(and potentially changes) everything.  If you want to simulate pure POPC to 
verify that things are fine, do that.  But taking more time on any perceived 
discrepancies here is not productive.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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