[gmx-users] Re: Topology and mdp file for coupling vdw and coulombic interactions for running FE calculations using BAR

[Justin Lemkul]

On 9/17/12 3:38 PM, Sonia Aguilera wrote:
> Hi Justin,
>
> So, are you saying that I should use my topoly file with all the original
> charges for both none-vdw and vdw-vdw-q calculations? I understand that the
> couple-lambda* setting dictate which parameters are involved in both
> calculations. However, in your tutorial you set all charges to zero with the
> same settings in the mdp file. Can you please make this clear for me? Should
> I use the topoly file with the original charges for both calculations?
>

Yes, the topology can be complete with charges.  They were zeroed out in the 
tutorial because (1) those were the files provided with an old Gromacs tutorial 
(for version 3.3.1) and (2) it was conceptually easier.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
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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