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

[Justin Lemkul]

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

-- 
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Justin A. Lemkul, Ph.D.
Postdoctoral Associate

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
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Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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