AMBER Archive (2009)

Subject: Re: [AMBER] using ptraj

From: Molecular Dynamics (amberquestion_at_yahoo.com)
Date: Tue Feb 17 2009 - 05:44:09 CST

Dear Carlos,

I did the same proccess with the mdvel file, but ptraj didn't extract the snapshot that is the same with my foo.rst file. My ptraj input files are

trajin equ.mdcrd 200 200 1 ( It worked fine )
trajout foo.rst restart

trajin equ.mdvel 200 200 1 ( I didn't get velocity.rst file )
trajout velocity.rst restart

What is the reason of it ?

Regards

________________________________
From: Carlos Simmerling <carlos.simmerling_at_gmail.com>
To: amberquestion_at_yahoo.com; AMBER Mailing List <amber_at_ambermd.org>
Sent: Monday, February 16, 2009 10:41:54 PM
Subject: Re: [AMBER] using ptraj

it can be done with ptraj and a bit of extra work, but the important
thing is that you need to have saved velocities separately in the MD,
they are none in the coordinate trajectory file. if you set ntwv to
the same as ntwx, it can be done.

On Mon, Feb 16, 2009 at 3:31 PM, Molecular Dynamics
<amberquestion_at_yahoo.com> wrote:
> Dear All,
>
> Is it possible to extract a snapshot ( coordinates, box size and alpha, beta gamma angles information ) with velocity information from any Amber trajectory files with ptraj and saving this like a restart file ?
>
> Regards,
>
>
>
>
>
>
>
>
>
>
>
> hasEML = false;
>
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>

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