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

neeru sharma neeru.bioinfo at gmail.com
Wed Jul 4 17:38:37 CEST 2012

Thanks Justin for your early response. I was confused about it, but
now it's clear. Thanks


> 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.


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