[gmx-users] Normal-mode analysis in Gromacs

David van der Spoel spoel at xray.bmc.uu.se
Thu Mar 8 07:29:09 CET 2018

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

David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.

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