[gmx-users] g_wham cycl or periodic

[Justin Lemkul]

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

-- 
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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 601
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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