[gmx-users] Gromacs 5 umbrella sampling

[Justin Lemkul]

On 4/7/14, 10:35 PM, Andres Ortega Guerrero wrote:
> Thank so much Justin for the help, I am going to reinstall gromacs 5 and try,
> I decided to install gromacs 4.6.5, and instead of a flat  bottom potential ,
> uses position restraint in x and y , in order to get the pmf of a drug
> passing throughout of an ion channel , I don't know if this could affect that
> much due to this bias(do you think so?) , but If I have time try to get both
> using gromacs 5 ,
>

In theory, using "normal" position restraints in x and y should be fine, just 
note that g_wham won't know how to deal with that information so you'll have to 
use an external WHAM implementation to construct the PMF.

-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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