[gmx-users] Normal mode analysis of pure water

Justin A. Lemkul jalemkul at vt.edu
Tue Oct 20 15:37:47 CEST 2009

simon sangma wrote:
> Hi  Justin,
>                 I tried  altering  the  .mdp file  (integrator  =  
> steep  instead  of nm) for energy  minimization. But in that case the 
> mdrun did not generate the Hessian matrix (nm.mtx) inspite of using the 
> command twice.

Energy minimization is not the same thing as Normal Mode Analysis.  You have to 
energy minimize your system (thoroughly!) first, then run NMA.


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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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