[gmx-users] Semiisotropic pressure coupling

[shivangi nangia]

Hello Justin,

I have a follow up question.

The non-bonded parameters you have pointed out to :
http://www.gromacs.org/Documentation/Terminology/Force_Fields/CHARMM

is valid if the system contains only lipid or it should be use with a
system containing lipid and protein too.

Thanks,

sxn


On Mon, Feb 16, 2015 at 2:10 PM, shivangi nangia <shivangi.nangia at gmail.com>
wrote:

> Thanks a lot Justin!!!
>
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> 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
>>
>> ==================================================
>>
>
>