[gmx-users] Umbrella Sampling and histograms smoothness

Agnivo Gosai agnivogromacs14 at gmail.com
Tue Feb 10 02:55:43 CET 2015

Dear Users

Dr. Lemkul , thanks for the suggestions. I am using pdb2gmx for generating
the topology and the itp files. Therein , automatic position restraints are
generated. Now, I have never used manual restrain force constants.

Could any user suggest any source / literature for choosing "restraint
forces" for DNA/protein systems ?

Regarding window setup, is it the spacing of the windows ?

Except for simulation time is there any other method for increasing
sampling ?

I have read the manual but could not find anything. I am searching in the
web also.

Thanks & Regards
Agnivo Gosai
Grad Student, Iowa State University.

On 2/9/15 4:11 PM, Agnivo Gosai wrote:

> Dear Users
> My umbrella sampling simulations are of 1 ns time whereas Dr. Lemkul's
> tutorial advocates a 10 ns simulation time. I found that after running WHAM
> , my histograms are coarser ( rough) compared to Dr. Lemkul's. A few of my
> histograms have two peaks!!
> So should I increase the simulation time from 1 ns to 10 ns ?? I do a 100
> ps NPT equilibration and then a 1 ns umbrella sampling in each of my
> windows. The generated PMF curve is also not smooth and is discontinuous at
> one position which I think I can fix by adding more windows around that
> co-ordinate.
> A picture is linked : ​
> <
> https://docs.google.com/file/d/0B-U8uULVZjfRQXcyUkI2bXhBcVE/edit?usp=drive_web
> >
>> Kindly help.
You need to assess convergence like you would for any type of system.  Most
of your peaks look rocky, so that generally indicates insufficient
sampling, poor window setup, suboptimal restraint force constant, or some
combination of those.

Don't think that 10 ns is some magic number, either.  It worked for that
system after I did a bunch of checking and the result was converged.  Some
umbrella sampling takes way more time.



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


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