You can use cpptraj or ptraj to create restart files from the mdcrd:
trajin my_traj.mdcrd 5 100 5
trajout my_snapshots.restrt restart
However, note that you will *not* have any velocity information, so it can
never be a true restart. Therefore, you may be better off using the restart
that has been working for you, but just looks weird.
HTH,
Jason
On Mon, Aug 15, 2011 at 10:32 PM, Bruno Rodrigues <bbrodrigues.gmail.com>wrote:
> Dear all,
>
> I'm running a long simulation of DNA and water, with 20 different inputs.
> However, at the 19th, the simulation stopped, and did not restart.
>
> I searched on the list and found that, because I didn't use iwrap, maybe
> there are some coordinates very far from the origin and sander didn't read
> it.
>
> However, if I use iwrap, it messes out the DNA inside the box. I managed to
> bring the molecules back to the box by centering them. But how can I
> generate a restart file from the mdcrd ones?
>
> Regards,
>
> --
> --
> Bruno Barbosa Rodrigues
> PhD Student - Physics Department
> Universidade Federal de Minas Gerais - UFMG
> Belo Horizonte - Brazil
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Tue Aug 16 2011 - 04:30:03 PDT
