Thank you Bruno,
I get it done now.
Best regards,
Catherine
> Date: Sat, 24 Sep 2011 09:37:50 -0300
> From: bbrodrigues.gmail.com
> To: amber.ambermd.org
> Subject: Re: [AMBER] How to recover rst or can I readin mdcrd for a MD by -c?
>
> 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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> >
>
>
>
> --
> --
> 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 - 23:30:02 PDT
