C Johnson wrote:
If you're proceeding blindly, then you're likely going to frustrate yourself to
no end. There is literature relevant to what you're doing - pulling on
peptides/proteins to unfold them is something that's been done. So you should
have some methodological precedent.
"Non-Protein" is a default group that should have been written to the .ndx file
by make_ndx. The only reason I can see for this error to come up is if you've
removed it from the pull.ndx file. If you're using my .mdp file, then
Non-Protein is a temperature coupling group.
-Justin
I know there is literature relevant but is there any that explains how to do it in Gromacs?
I don't know. All I implied was that some of the mystery can be taken out of
the process. A good Methods section can be translated to the parameters needed
by Gromacs as input. Usually "how-to" material is reserved for tutorials, not
the literature.
-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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