[gmx-users] Replicating and equilibrating DPPC 128 lipid. pdb

[Justin Lemkul]

On 11/19/14 7:13 AM, Priya Das wrote:
> I used dppc.128 (128 DPPC lipids and 3655 water molecules) for replicating
> .
>

If it's from Peter Tieleman's site, the PBC is a problem, because those 
molecules are "broken" (i.e. all put within the box).  You need to correct for 
this with trjconv and a suitable .tpr that defines the bonded connectivity.

-Justin

-- 
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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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