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.
-Justin
----- Original Message -----
From: Justin Lemkul <jalem...@vt.edu>
To: Abed Askari <abedask...@yahoo.com>; Discussion list for GROMACS users
<gmx-users@gromacs.org>
Cc:
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
--
==================================================
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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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