vidhya sankar wrote:
Thank you Dr Justinj,
To do SMD should i create centre of mass
of my reference (protein) and pull group (ligand)? if i need to create ,
which tool of gromacs generate to be used .?
How to include this center of mass in SMD .mdp files
None of this is necessary. Gromacs does all COM calculations internally.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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