[gmx-users] Normal Mode Analysis

[Adip Jhaveri]

Thank you for the response.
But how will the system be affected when I remove the constraints? I am
trying to get a measure of the entropy by the normal mode analysis, so will
removing the constraints lead to an incorrect estimation?

Regards,
Adip

On Thu, Oct 17, 2019 at 4:06 AM David van der Spoel <spoel at xray.bmc.uu.se>
wrote:

> Den 2019-10-16 kl. 23:31, skrev Adip Jhaveri:
> > Hello All,
> > I am simulating two proteins in solution and would like to perform Normal
> > Mode Analysis on trajectory snapshots.
> >
> > I take one particular frame in the trajectory and minimize it, followed
> by
> > mdrun for normal mode analysis. However I am getting constraint errors in
> > each of the two steps -
> > 1) In minimization it is recommended to use 'cg' method but this does not
> > work and it throws an error due to the constraints present in the system.
> > 2) I tried using the 'steep' method for minimization but then, during the
> > normal mode mdrun, it is giving an error on constraints. How do I solve
> > this problem? Do I completely remove the constraints and then perform
> 'cg'
> > minimization and 'nm' mdrun?
> Yes.
>
> >
> > Regards,
> > Adip
> >
>
>
> --
> 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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