Aw: [gmx-users] Umbrella sampling- force vs time plots

Justin Lemkul jalemkul at
Wed Jul 10 12:49:48 CEST 2013

On 7/9/13 7:38 PM, rookie417 wrote:
> Thanks Justin and Stephan,
> One more question, while pulling from the interior of a multiple monomer
> micelle structure, I used higher force  constants (5000 kJ/mol/nm^2) for
> position restraints on the reference group to keep the system intact. I am
> assuming that I have to use different pull_k1 for inside and outside the
> structure, due to the nature of interactions. Is that correct? I was also

Not necessarily.  See Thomas' reply here for a nice explanation of changing 
force constants.

> wondering how g_wham evaluates the PMF for the multiple interactions inside
> the system considering the position restraints and pull force constant.

I would suggest you read the g_wham paper, where the program is described in detail.



Justin A. Lemkul, Ph.D.
Postdoctoral Associate

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 | (410) 706-7441


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