[gmx-users] (no subject)

A. A. Jeyaprakash jprakash at mbu.iisc.ernet.in
Wed Jul 7 09:06:47 CEST 2004

Dear Gromacs Users,

      Being a new user of the MD technique and Gromacs, I have a 
couple of questions for which I need directions to look in. 

      If I would like to study the dynamics of the ligand binding site
alone (in other words, If I want to keep the major part of the protein
structure rigid) where do I need to instruct GROMACS? and In that case do
I need to solvate the whole system or the solvation of the region of
interest (ligand binding site) is sufficient?

      Is it possible to make a desired Angstroms (say, 12 Angstroms) of
water cap around the region of interest without defining the box? If so 
how should I instruct Gromacs.

      Thanks in Advance,

with regards,

A. Arockia Jeyaprakash, 
Research Associate, Molecular Biophysics Unit,Indian Institute of Science, 
Bangalore-560 012 INDIA
Ph: +91-80-22932389 Fax:+91-80-23600535

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