I guess it depends a lot on what you want to do. If you just need the
atomic coordinates, you could save them all as a pdb trajectory (I'm not
familiar with ptraj, but I imagine this is possible). That way VMD will
read it without the need for your prmtop file, and you can not have all the
waters and ions. There may be some analysis limitations to this though, as
you don't have the full information anymore. Perhaps Marc's suggestion is
better for that reason.
Another option might be to simply reduce the number of steps you have.
That is, you could delete every other frame. Depending on how often you
were taking snapshots, and the autocorrelation time of the variables you
are interested in, a lot of those snapshots may be valueless.
Finally, are those binary netCDF trajectories (ioutfm=1)? If not I suggest
converting them, they tend to take up ~50% as much space and load far
faster also. I'm not sure how the hard drive space used would compare
against a regular formatted trajectory that has been zipped, but for memory
purposes the zipping is irrelevant.
~Aron
On Thu, Mar 8, 2012 at 10:53 AM, Marc van der Kamp <marcvanderkamp.gmail.com
> wrote:
> Hi Catherine,
>
> You can load a pdb file without water and Na+ into VMD before loading the
> mdcrd - the pdb file you can make using ptraj if you like.
> Alternatively, go back to tleap/sleap/xleap and write a prmtop without
> water and Na+ and use that.
>
> --Marc
>
> On 8 March 2012 15:47, Catein Catherine <askamber23.hotmail.com> wrote:
>
> >
> > Dear Sir,
> >
> > I have a large number of mdcrd files. I need to view and analysis all
> > these files in one goes with VMD. However, due to the memory reason, I
> > cannot load all these files to VMD.
> >
> > Could you mind to suggest how to use ptraj to convert all these files to
> a
> > format that readable in VMD with less memory.
> >
> > I think of using ptraj to convert all these mdcrd files to single mdcrd
> > without water and Na+. However, after doing it, the inonegoes.mdcrd is
> > reduced by ten times. But I cannot read this file with VMD using my
> > original *.prmtop (after or after adding water or Na+) anymore. How to
> do
> > it properly? Please help.
> >
> > trajin ../1.mdcrd.gz
> > trajin ../2.mdcrd.gz
> > trajin ../3.mdcrd.gz
> > trajin ../4.mdcrd.gz
> > trajin ../5.mdcrd.gz
> > trajin ../6.mdcrd.gz
> > trajin ../7.mdcrd.gz
> > strip :WAT
> > strip :Na+
> > trajout inonegoes.mdcrd nobox
> >
> >
> >
> >
> >
> >
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo
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Received on Thu Mar 08 2012 - 08:30:05 PST
