[gmx-users] window spacing in umbrella sampling

[Justin Lemkul]

On 1/6/17 2:22 PM, faride badalkhani wrote:
> Dear GROMACS users,
>
> I have performed pulling simulations on polymer-drug complex an each window
> was obtained by an increment of 1 Å from the previous window, and for each
> window, 5 ns MD simulation was performed. But the histogram for the first 6
> windows is as follows:
>
> https://www.dropbox.com/s/2yzmbyl2nrt6hwq/histo.xlsx?dl=0
>
> I am very beginner in Umbrella sampling. Could you tell me how should I
> change the sampling to get a reasonable histogram, please?
>

The windows are not evenly spaced and/or the force constant is insufficient to 
maintain the desired restraint distances.  You have mostly redundant windows 
with a huge gap.  You may need more windows, better/different spacing, and/or 
different force constants.

-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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