[gmx-users] constraint pulling
jalemkul at vt.edu
Mon Mar 17 16:12:07 CET 2014
On 3/17/14, 10:52 AM, leila karami wrote:
> Dear gromacs users
> I will use pull = constraint (constraint pulling) for PMF calculations.
> There is a tutorial about PMF from Justin in which he used
> pull = umbrella (umbrella sampling).
> In justin tutorial, step are as follows:
> 1) preparation of system
> 2) minimization & equilibration
> 3) generate configuration
> 4) umbrella sampling
> 5) WHAM which gives PMF curve
> I conceive in my case (pull = constraint), steps 1, 2 and 3 are similar to
> justin case (pull = umbrella). Since, WHAM analyzes output files
> generated by umbrella sampling, I have not idea about steps 4 and 5.
> I did not know how to obtain PMF curve in my case.
> If my notion is wrong, please give me more explanation such that I do
> this PMF calculation using constraint pulling method. Please tell me steps
> needed for
> constraint pulling.
> Is there a tutorial about PMF calculation using constraint pulling method?
If you're using a constraint to preserve distances along the reaction
coordinate, there's nothing to de-bias. There is no force constant for
constraint pulling, so you can't run WHAM on its output. The constraint method
fixes the distance, whereas the umbrella method is a harmonic bias (which is
what you need for umbrella sampling, hence the name). If you did the "umbrella
sampling" with the constraint method, there's nothing you're going to get out 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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