Re: [gmx-users] Normal-mode analysis in Gromacs

[Kevin C Chan]

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.

Thanks,
Kevin


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.
> http://www.icm.uu.se
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[gmx-users] Calculation of potential of mean force between sodium and chloride ion pair in water using replica exchange umbrella sampling in gromacs

[Mayank Dixit]

Dear Gromacs Users,
I would like to calculate the potential of mean force between sodium and
chloride ion pair in water using replica exchange umbrella sampling method
in gromacs. Please let me know the details of replica exchange umbrella
sampling in gromacs.

Thanks and kind regards
Mayank

 ​


*Dr. Mayank  Dixit *
Post-doctoral fellow
Department of Chemistry
The city college of New York
Marshak Science Building
160 convent avenue 138th street.
New York, NY-10031
Cell no: 16465894905
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