Den 2018-03-08 kl. 00:53, skrev Kevin C Chan:
Dear Users,

I have encountered several questions when I try to perform NMA on a protein
structure from an equilibrated MD simulation. I were basically referred to
the gromacs manual (
http://www.gromacs.org/Documentation/How-tos/Normal_Mode_Analysis) and some
threads in the mailing list.

First, Gromacs (and in some literature) suggest to have L-BFGS energy
minimization (sometimes after steep and cg calculations) of the structure
before NMA and L-BFGS generally requires shifted/switched interactions.
However, for vdW the option should have been changed by introducing the
vdw-modifier and l-bfgs seems to still recognize it as cutoff.

Second, for electrostatics, the option has been improved by
Reaction-field-zero but is it still suitable for NMA calculation?

Third, I have achieved a maximum force of 9.78750e-01 using cg and still
got the warning: "The force is probably not small enough to ensure that you
are at a minimum." Usually how stable do we have to achieve in order to
avoid the warning?

Thanks in advance for any experience shared.
You need to compile gromacs in double precision to get to low forces.


Kevin
OSU Pharmacy



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Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
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