[gmx-users] constraint pulling

[Justin Lemkul]

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

-- 
==================================================

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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