[gmx-users] Semiisotropic pressure coupling

[shivangi nangia]

Thanks a lot Justin!!!






On Sun, Feb 15, 2015 at 1:13 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>
> ==================================================
>