[gmx-users] Normal mode analysis of pure water

Justin A. Lemkul jalemkul at vt.edu
Tue Oct 20 16:22:26 CEST 2009

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 


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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


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