[gmx-users] PMF calculation with constraint distance

[Justin Lemkul]

On 5/21/15 5:19 PM, leila salimi wrote:
> Thanks Justin. Yes I have done PMF with Blue moon ensemble with DFT. Now I
> want to do the same with gromacs to have some knowledge  about my FF
> parameters and compare with my DFT results!
> You meant I have to do with different configuration and average the forces?
> I am wondering that I did in DFT for each constrained distances around 15
> ps MD and then I used averaged forces for each distances!
>

I don't know what your QM involved; when I hear "Blue moon" I think of the 
beverage - cheers! :)

If your QM gave you an energy vs. time plot, that's not a PMF.  That's a 
potential energy scan with some fixed intermolecular geometry.  Again, maybe I 
just don't know what you're doing.  In principle you could do the same thing 
with a rigid constraint between the groups, but your post is a bit confusing.

-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 629
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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