[gmx-users] Regarding parameters for pull_groups in mdp file for the pull code

[Justin A. Lemkul]

On 7/4/12 2:31 AM, neeru sharma wrote:
> Dear Gromacs Users,
>
>
> I have some queries about the parameters in the .mdp file for the pull code.
>
> If I want to pull my ligand, towards specific atom/group of atoms from
> the protein, how am I supposed to mentioned these in the mdp file?
>
> *****************************************************************
>   pull                 = umbrella
>   pull_geometry  = distance
>   pull_start         = yes
>   pull_ngroups    = 1
>   pull_group0     = Ligand
>   pull_group1     = Atom/group of atoms from the protein
> *****************************************************************
>
> Here, I want to specify the pull_group0 as "Ligand" and pull_group1 as
> "Atoms of the protein".  My query is regarding these groups. Shall I
> just write the name of the Ligand and Atoms (specifying the atom no)
> or am I supposed to create a separate index file for each of them (one
> for ligand and other for group of atoms) ?
>

All groups specified in the .mdp file must be either valid default groups or 
custom groups provided in an 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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