[gmx-users] umbrella sampling tutorial

Ming Tang m21.tang at qut.edu.au
Tue Apr 7 13:11:14 CEST 2015

Hi, Justin

I am working with a triple helix using umbrella sampling method. When generating configurations, I pulled 1ns (md_pull.mdp). Then I got 15 configurations using 0.03 spacing. They are conf0.gro conf5.gro conf10.gro conf15.gro conf17.gro conf18.gro conf30.gro conf31.gro conf39.gro conf59.gro conf87.gro conf161.gro conf233.gro conf360.gro conf488.gro. Most of the configurations are within 0-100 frames. Does this affect the umbrella sampling simulations? Is there any pulling time requirement when generating the configurations?  I was supposed to have a try and find the result, but found that the calculation is time-consuming. So I decided to ask you finally.

Thanks a lot,

-----Original Message-----
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of Justin Lemkul
Sent: Wednesday, 18 March 2015 9:45 PM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] umbrella sampling tutorial

On 3/17/15 9:06 PM, Ming Tang wrote:
> Hi Justin,
> Thanks a lot. I can move forward now.
> Recently, I am trying to pull  a triple helix, and want to fix the center of mass of the three terminal atoms. One paper said that it can be done by means of a strong harmonic restrain with a super large spring constant in Gromos96 53 a6. But I still don't know how to do this.  Can you give me some advice?

Absolute restraints can be used in the pull code, but I've never done it.  Note that such an approach is incompatible with NPT.  Freezing may also be an option, but then you're acting directly on all the atoms and frozen groups carry their own artificiality.



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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