[gmx-users] Normal-mode analysis in Gromacs

[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.

Kevin
OSU Pharmacy