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

neeru sharma neeru.bioinfo at gmail.com
Wed Jul 4 08:31:15 CEST 2012

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) ?

Any suggestion is welcome!!

Thanks in advance.


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