[gmx-users] g_wham cycl or periodic
jalemkul at vt.edu
Fri Aug 8 22:57:33 CEST 2014
On 8/8/14, 2:41 PM, ANDRES ADOLFO ORTEGA GUERRERO wrote:
> Hi Dear Gromacs User,
> I was wondering if you could help me explaing something, i usea g_wham for
> a PMF calculation of a molecule passing through an ion channel, i use the
> option cycl and periodic, i think the cycl is the right choice?, but i dont
> understand the concept of if my calculations are periodic or cyclic. Could
> you help me with this.
The use of -cycl implies that the free energy at the minimum and maximum value
of the reaction coordinate is the same. Your situation should qualify, because
your molecule will have (theoretically) zero interaction at long distances away
from the channel on either side of it.
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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