[gmx-users] Normal Mode Analysis

Erik Lindahl lindahl at cbr.su.se
Wed Jul 4 08:50:19 CEST 2007


First, it's just a warning that the force _might_ not be small enough  
since there's no bullet-proof way to say.

In general, both for final-stage energy minimization (with L-BFGS)  
and actual normal mode analysis you can use a setup with

double precision
switched coulomb & vdw interactions; cutoffs e.g. at 1.0 nm, switched  
from 0.8 nm (or shifted from 0 nm).
rlist at 1.2 to 1.3

It is imperative that you use the -t option to grompp when you create  
the NM run input file, so you read full precision binary coordinates  
and not the three-decimal gro file.



On Jul 4, 2007, at 8:37 AM, Anirban Ghosh wrote:

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