[gmx-users] Normal mode analysis of pure water

[Justin A. Lemkul]

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

> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

-- 
========================================

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

========================================