Recent versions of cpptraj will keep all velocity information from
input trajectories. Make sure you're using the most up to date version
of cpptraj. I know that there is an older binary (non-NetCDF) version
of the restart format, and that is not currently supported. If this is
what you have I will need to release an update. If you have a NetCDF
restart file you should be fine.
-Dan
On Thu, Nov 17, 2016 at 5:54 PM, Nhai <nhai.qn.gmail.com> wrote:
> Besides cpptraj, You can use ncdump program (already in amber) to get any info (velocity, force, ...) you want.
>
> Check ncdump ---help
>
> Hai
>
>> On Nov 17, 2016, at 4:39 PM, giulia palermo <giulia.palermo83.gmail.com> wrote:
>>
>> for using the information in an other code.
>>
>>
>>
>>
>> 2016-11-17 12:58 GMT-08:00 Hai Nguyen <nhai.qn.gmail.com>:
>>> just curious: why do you need to convert to human readable format?
>>>
>>> Hai
>>>
>>> On Thu, Nov 17, 2016 at 1:55 PM, giulia palermo <giulia.palermo83.gmail.com>
>>> wrote:
>>>
>>>> Dear all,
>>>>
>>>> I am trying to extract coordinates and velocities from the binary
>>>> .rst7 file, which is produced from MD runs with AMBER, and converting
>>>> it into a readable rst7 file.
>>>> I have been using the follong command successfully with previous
>>>> versions of AMBER (using ptraj). In the new version ptraj is
>>>> substituted by cpptraj. However, the command should in principle work
>>>> and provide me an rst7 file including coordinates and velocities.
>>>> The coommand I am using is the following:
>>>>
>>>> cpptraj SYS.prntop <<EOF
>>>> trajin SYS.rst7
>>>> trajout SYS_new.rst7 RESTART
>>>> EOF
>>>>
>>>> As a result, I obtain a file which only includes coordinates. However,
>>>> I need the velocities, too.
>>>>
>>>> Can you please help me in getting it?
>>>> The amber rst7, produced upon MD run, shoul contain the velocities,
>>>> otherwise the MD engine would not be able to pursue dynamics.
>>>> It seems a matter of how extract them in a readable (not binary) rst7
>>>> format.
>>>>
>>>> Thank you very much
>>>> Giulia
>>>>
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>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>
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>>
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--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Thu Nov 17 2016 - 15:30:04 PST
