Dear Catherine,
This subject has been discussed before here at the list, but I can summarize
it for you:
1 - You can generate a restart file from your mdcrd:
trajin my_traj.mdcrd Last_frame
trajout my_snapshots.restrt restart
2 - The dynamics will change. " This is true even if you keep
the same velocities and just change the random seed on a stochastic
thermostat or barostat, since such systems are chaotic by nature (so it is
not necessarily a problem). The problem with using a ptraj-generated
restart file (which doesn't *really* have no velocity information, all
velocity components of all atoms are set to 0), is that your temperature
drops to 0 at that point, in which case you have to wait for your system to
heat back up before you can claim that collected snapshots are members of
your desired ensemble. If you have a restart file from a previous step (the
last restart file that worked), just use that one" copied from Jason's
reply.
On Fri, Sep 23, 2011 at 11:18 PM, Catein Catherine
<askamber23.hotmail.com>wrote:
>
> Dear Sir/Madam,
>
> I have to accidentally removed by restrt files after running a series of
> MD. Is it possible to recover a restrt or another file format from the out
> or mdcrd files so that I can get continuous running the MD and put this
> recoveried file after -c xxx.
>
> Best regards,
>
> Catherine
>
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
--
Bruno Barbosa Rodrigues
PhD Student - Physics Department
Universidade Federal de Minas Gerais - UFMG
Belo Horizonte - Brazil
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Received on Sat Sep 24 2011 - 06:00:03 PDT
