[gmx-users] Langevin Dyanamics in GROMACS

[M Hafizur Rahman]

Hi Justin:
Thanks for your reply.
More spicifically, I still need to know how the value of friction 
coefficient goes.
and also how PMFs of every pairs of ions goes. I am not actually asking how 
to create PMF at this moment.

Thanks,
M. H. Rahman

----- Original Message ----- 
From: "Justin A. Lemkul" <jalemkul at vt.edu>
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Sent: Friday, February 13, 2009 5:51 PM
Subject: Re: [gmx-users] Langevin Dyanamics in GROMACS


>
>
> M Hafizur Rahman wrote:
>> Hi all:
>> Anyone can help me using Langevin Dynamics in GROMACS. Where does the 
>> friction coefficient goes and How we can change the forece field to 
>> include PMF.
>>
>
> For Langevin dynamics, read manual sections 3.8 or 3.9, depending on what 
> you want to do.  Associated run control parameters are in section 7.3.3, 
> or online:
>
> http://www.gromacs.org/documentation/reference_4.0/online/mdp_opt.html
>
> As for PMF, read manual sections 6.1, 6.3, and/or 6.4.
>
> -Justin
>
>> Thanks,
>> M. Rahman
>>  ------------------------------------------------------------------------
>>
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> -- 
> ========================================
>
> Justin A. Lemkul
> Graduate Research Assistant
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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