[gmx-users] regarding umbrella sampling
jalemkul at vt.edu
Mon Aug 19 22:45:06 CEST 2013
On 8/19/13 4:35 PM, Abed Askari wrote:
> thank you for your reply.
> because without the position restraint the cylindrical shape of my molecule (CNT)
> changes. is it reasonble to use umbrella sampling along with the position restraint in
> y and z directions?
Possibly, but it sounds more like your umbrella restraint is causing
deformations in the CNT, so either the umbrella restraint is inappropriate or
the CNT topology is not stable. I would investigate those options first before
applying several layers of bias.
> ----- Original Message -----
> From: Justin Lemkul <jalemkul at vt.edu>
> To: Abed Askari <abedaskari at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org>
> Sent: Tuesday, August 20, 2013 12:42 AM
> Subject: Re: [gmx-users] regarding umbrella sampling
> On 8/19/13 4:03 PM, Abed Askari wrote:
>> Dear gmx-users
>> I want to use umbrella sampling to calculate the PMF between
>> two molecules and x-axis is the reaction coordinate. would you please
>> tell me I can use position restraint in y and z directions for the pulling group or not?
> Why would you need to? In general, position restraints and an umbrella
> restraint are not simultaneously necessary. Sometimes they are, but usually not.
Justin A. Lemkul, Ph.D.
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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