[gmx-users] Coordinate file for charmm36 POPC
jalemkul at vt.edu
Thu Aug 14 14:33:09 CEST 2014
On 8/14/14, 8:29 AM, yashita thakur wrote:
> Thank you Ariel for your reply.
> How to know what should be the size of system.
> Like it should be 30,000 or more. Then how to mention it.
> secondly how to know how many lipid POPC should be added. In united-atom
> Berger model from Peter Tieleman POPC number is 128.
> Should I ass that much or more that that??
> Can I use Peter's coordinate file deleting water and follow the same step
> as mention in Justin A. Lemkul tutorial??
If you want to use CHARMM36, then no, you should not use united-atom lipids
equilibrated under a different force field. You can get a suitable CHARMM36
membrane from http://terpconnect.umd.edu/~jbklauda/research/download.html
The size of the membrane patch depends on the size of the protein you need to
simulate. For modest-sized proteins, 128 lipids is enough. For larger
proteins, you will need to extend the membrane using genconf or genbox.
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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