AMBER Archive (2009)

Subject: Re: [AMBER] using ptraj

From: Molecular Dynamics (amberquestion_at_yahoo.com)
Date: Tue Feb 17 2009 - 08:11:16 CST

Dear Carlos,

I tried the procedure with the trajin.in file

trajin equ.mdvel 10 10 1
trajout velocity.rst restart

I got the restart file . I think I should write the frame number when using mdvel file in ptraj input file. And I should determine the frame number according to the nstlim step for the coordinates I want to extract as restart . Could you give me some information about it ?

Regards

________________________________
From: Carlos Simmerling <carlos.simmerling_at_gmail.com>
To: AMBER Mailing List <amber_at_ambermd.org>
Sent: Tuesday, February 17, 2009 2:37:15 PM
Subject: Re: [AMBER] using ptraj

what did ptraj say it was doing in the output?

On Tue, Feb 17, 2009 at 6:44 AM, Molecular Dynamics
<amberquestion_at_yahoo.com> wrote:
> 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;
>>
>>
>>
>>
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>>
>
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