[gmx-users] Umbrella sampling - position restraints

Justin Lemkul jalemkul at vt.edu
Thu Aug 8 22:00:23 CEST 2013

On 8/8/13 3:57 PM, rookie417 wrote:
> Dear GROMACS users,
> I followed the Umbrella Sampling tutorial to run a simple simulation of
> pulling polymer chain from the surface of micelle. I used position
> restraints for the initial equilibration, however I realized a typo in the
> define=-DPOSRES mdp files for pulling, US_NPT and US_MD simulations later
> during analysis. The simulations ran normally and the PMF plots look
> accurate. However, I realized that position restraints were not applied only
> after looking at the log files and position restraints energy values were
> missing. The umbrella sampling MD simulation was for 2 ns only and I checked
> the pullx-umbrella.xvg files and the COM fluctuations are not that bad
> considering its only a short time for convergence.
> Can anyone comment on how not using position restraints would effect the
> result otherwise?

Position restraints are generally not necessary.  Please refer to our paper that 
is associated with the umbrella sampling tutorial to understand why we used them 
in this particular case.



Justin A. Lemkul, Ph.D.
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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