[gmx-users] regarding umbrella sampling

[Justin Lemkul]

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 <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.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
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