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
--
========================================
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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