[gmx-users] Normal Mode Analysis
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
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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