Thanks to all of you. Sorry for the late reply. I am trying the MD
simulation again following all of your suggestions. Thanks again.
Anindya
On Fri, Dec 17, 2010 at 8:52 PM, Jason Swails <jason.swails.gmail.com>wrote:
> On Fri, Dec 17, 2010 at 2:55 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
>
> > > I have started MD simulation of two proteins with the AMBER package.
> But
> > I
> > > have faced one problem during running of AMBER MD simulation. After the
> > run
> > > of the first 5ns one, the coordinate files over 5000 trajectories were
> > > really big and those are difficult for handling because I think those
> > > contain the coordinate, velocity and energy informations. To get rid of
> > this
> > > problem, can anybody suggest me how I can generate the coordinate,
> > velocity
> > > and energy informations in separate files. I need only the trajectories
> > in
> > > the coordinate files. I am wondering if I give the output coordinate
> file
> > > extension from crd to mdcrd whether it will help or not.
> >
> > Mdcrd files only contain coordinates.
> > Mdvel files only contain velocities.
> > Mden files only contain energies, but if you use it be sure to check
> > these against mdout, which is more used for energies.
> >
> > Netcdf is recommended for mdcrd, and likely works for mdvel. I believe
> >
>
> Minor comment here. It definitely works for mdvel. In fact, it's the only
> form mdvel files can take (perhaps because they're more likely to bust out
> of the size limit imposed by f8.3 fixed format?)
>
> Aside from this (mostly) meaningless contribution, Bill's explanation is
> both thorough and correct.
>
> All the best,
> Jason
>
> it is more compact (being binary), and in any case should be higher
> > precision.
> >
> > You can select every nth frame to create a smaller mdcrd using ptraj.
> >
> > > Other thing is that I can not see the continuous increment of the
> output
> > > files during the run and I am getting only the files after the complete
> > run.
> >
> > What is your run environment? Parallel/serial? In serial nonbatch at
> least,
> > you should see the files grow.
> >
> > > Can anybody help me that I should include any particular command in the
> > > execution file (having extension .in) and where it should be placed in
> > the
> > > file to see the file progressions during the MD runs.
> >
> > Maybe this is a parallel or batch phenomenom, appropriate for batch job
> > settings.. not sure.
> >
> > > I have another question that for coordinate files whether there are any
> > > differences among crd, inpcrd and mdcrd extensions and same for the
> > > parameter files also which are prmtop and parm7 ones. I am not sure
> which
> > > one I should use for the MD simulation runs.
> >
> > The extensions are just for convenience and have no effect on how
> anything
> > runs. You could have no extensions if you like. If you use .mdcrd for
> > mdcrd files, it will remind you what they are. Inpcrd and restrt are the
> > same format, except inpcrd is unlikely to contain velocities. Restrt is
> > the only format containing coordinates, velocities, and box info, and in
> > ascii format it is higher precision than the ascii format mdcrd. I'm
> > guessing that parm7 refers to an earlier version of prmtop.
> >
> > I hope that helps.
> >
> > Bill
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Tue Dec 21 2010 - 09:30:03 PST
