On 8/26/12 7:44 PM, Acoot Brett wrote:
Dear All,
I am still confused and I hope I can get some detailed explaination. For
example, I want to determine the interaction energy between residue 52 and
residue 105, how should I set energyggryp and what is the related commands?
And if I want to determine the interaction energy between residue 52 in China A
and residue 8 in Chain B, what will be the difference?
You can also tell me a internet link on it.
The help information from make_ndx is what you need. Type "help" at the prompt
(without quotes) and you will see examples.
For instance, to select residue 52 of chain A:
ch A & r 52
That creates a group that you can then use as an energygrp in the .mdp 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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