[gmx-users] Coordinate file for charmm36 POPC

Justin Lemkul jalemkul at vt.edu
Tue Aug 26 14:11:14 CEST 2014

On 8/26/14, 4:50 AM, yashita thakur wrote:
> Thank you Justin for you help.
> But I am asking about  Peter C. Lai POPC lipid which is for charmm36 force
> field please see the link below
> http://cesium.hyperfine.info/~peter/gromacs/popc36/
> Not Peter Tieleman as mention in your tutorial as it is for united atom.
> Can I use Peter C. Lai POPC lipid ???

Yes, those parameters appear to match what we have in our force field files.

> Another question is if I want to reduce some lipid from Peter C. Lai lipid
> Its 238 POPC but if I want only 200 then what is the command??

Use genbox to set a (smaller) box size.  It may be difficult to know what the 
exact dimensions should be, but fiddle with x and y until you get something 



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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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