[gmx-users] Normal-mode analysis in Gromacs

Kevin C Chan cchan2242-c at my.cityu.edu.hk
Thu Mar 8 23:44:06 CET 2018

Thank you David for your reply. In fact, I have already been using the
double precision version of Gromacs.

I will greatly appreciate it if other questions could also be covered.


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
> <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.
> http://www.icm.uu.se

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