[gmx-users] GROMACS command for energy calculation

[Justin Lemkul]

On 8/27/12 6:32 AM, Acoot Brett wrote:
> Hi Mark,
>
> Then MAP file has the ability to recognize the groups saved in the index file, which is in the same folder as the MDP file?
>

Any group specified in the .mdp file must be recognized by grompp (in the case 
of default groups) or otherwise supplied by the user via an index file passed to 
the -n flag of grompp.  It is not necessarily automatically recognized and can 
be in any location you like.

http://www.gromacs.org/Documentation/File_Formats/Index_File

-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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