[gmx-users] lipid molecules are overlapping with protein molecule

Justin Lemkul jalemkul at vt.edu
Tue Nov 11 13:38:29 CET 2014

On 11/11/14 6:45 AM, Padmani Sandhu wrote:
> Hello all,
> I am trying to energy minimize a trimeric protein in DPPC bilayer but
> facing problem in reaching desired lipid per area using "inflategro.pl".
> After 5 or 6 steps of shrinking and energy minimization lipids molecules
> start interfering with protein. I tried to increase cutt-off, but that is
> also giving error during grompp.

Proper energy minimization between shrinking steps should eliminate this.



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


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