Re: [AMBER] Generation of separate crd files

From: Jason Swails <>
Date: Fri, 17 Dec 2010 20:52:18 -0500

On Fri, Dec 17, 2010 at 2:55 PM, Bill Ross <> 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,

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
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Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
AMBER mailing list
Received on Fri Dec 17 2010 - 18:00:02 PST
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