AMBER Archive (2009)

Subject: Re: [AMBER] using ptraj

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Tue Feb 17 2009 - 08:29:07 CST

it is very important to make sure the velocities and coordinates are
from the same time point.
perhaps in your case it would be easier to take the coordinates and
let sander assign velocities in your restart. if you use ntx=1 it will
work- the only thing you may need to check is whether ptraj writes the
correct box size (if it was constant pressure run).
restarting from a trajectory frame is not trivial so you really need
to carefully study the file formats information on the amber web page.

On Tue, Feb 17, 2009 at 9:11 AM, Molecular Dynamics
<amberquestion_at_yahoo.com> wrote:
> 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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