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

Justin A. Lemkul jalemkul at vt.edu
Wed Jul 4 13:04:17 CEST 2012

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 A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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