[gmx-users] regarding umbrella sampling

[Abed Askari]

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?



----- 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>
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

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Justin A. Lemkul, Ph.D.
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