simon sangma wrote:
Hi Justin,
Are you suggesting that after thorough energy
minimization, seperate .mdp file is to be used for NMA? In that case how
would that output file (energy minimised file) be taken as an input file
for the grompp and mdrun command (for NMA)? What extension would the
file have (.what) ?
Yes, they are done in separate steps. I think you need to do some tutorial
material on the workflow of a GROMACS procedure. Run energy minimization (in
double precision), and the output of EM is your input for NMA (the minimized
structure).
-Justin
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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