I would suggest extracting data for multiple temperatures, and making sure
that you get a full set for each temperature and that the behavior varies
across temperatures. Which properties you choose to evaluate would depend
of course on your goals and on what your simulation is able to sample
during the REMD run.
On Mon, Nov 26, 2018 at 11:38 AM Rajarshi Roy <phd1701171011.iiti.ac.in>
wrote:
> Yes, But I extracted some frame from this mdcrd file and the output mdcrd
> file. Both of them are showing the same pdb structures. I think there
> something is wrong, Is there any other way to check that my simulation is
> doing well?
>
> On Sun, Nov 25, 2018 at 8:27 AM Thomas Cheatham <tec3.utah.edu> wrote:
>
> >
> > > Yes. I understand this. But my question is, if it is taking all the
> > mdcrd
> > > files, it should shows in the terminal that it is reading all of them.
> > Here
> > > is the output of my terminal,
> >
> > > INPUT TRAJECTORIES (1 total):
> > > 0: REMD trajectories (72 total), lowest replica
> 'remd_glycanC.mdcrd.001'
> > > (reading 4400 of 4400)
> >
> > It could be more verbose, but it does say above that it loaded 72 REMD
> > trajectories...
> >
> >
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> >
>
>
> --
> *with regards*
>
> *Rajarshi Roy*
>
>
> *PhD Research Scholar*
>
> *Biosciences and Biomedical Engineering*
>
> *Indian Institute of Technology, Indore*
> *India*
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Received on Mon Nov 26 2018 - 09:30:03 PST
