[gmx-users] ED-analysis

[Kavyashree M]

Dear Sir,

  Thanks for your patient reply Sir.

With Regards
M. Kavyashree

On Sat, Jun 11, 2011 at 9:57 PM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:

> Hi Kavya,
>
> >> It is absolutely necessary that the molecules be whole, and in the
> >> case of multimers, correctly assembled.
> >
> > But if there is only one polymer (protein) with water in the system
> > then also is it necessary to use nojump or mol in trjconv?because
> > in one of the mails -
> >
> > http://lists.gromacs.org/pipermail/gmx-users/2010-October/055320.html
> >
> > there was a discussion regarding this topic. So I wanted to
> > ensure regarding that aspect. Molecule after simulation
> > crosses the box boundary in the simulation I have done, So
> > if I processed analyzing with the native .xtc file there will be
> > a problem? But in this case its a single intact protein molecule
> > in water.
>
> That post concerns -pbc nojump. My reply to you was about having
> molecules in one piece. They're different things. Gromacs nowadays
> doesn't care about molecules being whole in the trajectory file, and
> happily writes them in pieces. So you can't be confident you can use
> the trajectory as is.
>
> Cheers,
>
> Tsjerk
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> post-doctoral researcher
> Molecular Dynamics Group
> * Groningen Institute for Biomolecular Research and Biotechnology
> * Zernike Institute for Advanced Materials
> University of Groningen
> The Netherlands
> --
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