Thank you so much all of you,
Those are valuable info you gave me. I will probably rerun my system
again with the addition of mdvel switch and using NetCDF file format.
best
peker
On Fri, Apr 15, 2011 at 12:36 AM, Jason Swails <jason.swails.gmail.com> wrote:
> On Thu, Apr 14, 2011 at 5:33 PM, peker milas <pekermilas.gmail.com> wrote:
>
>> Thank you Bill,
>>
>> Unfortunately i didn't run my simulation with mdvel option. If this is
>> the only way of having them, i need to run them again i believe.
>>
>
> Note you can't just put "-v mdvel" on the command-line to dump velocities.
> See the manual for the ntwv variable.
>
> Also note that velocities can be dumped *only* if you're using binary
> (NetCDF) file formats (ioutfm=1), and ptraj doesn't read velocities. You'll
> need to use ncdump (together with some scripting language, probably) in
> order to extract that information.
>
> HTH,
> Jason
>
>
>> best
>> peker
>>
>> On Thu, Apr 14, 2011 at 8:29 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
>> >> Recently i tried to find some documentation about how i can extract
>> >> momentum values from trajectory files. Unfortunately, i neither could
>> >> find a documentation nor figured out a way for extracting them. I
>> >> would like to ask whether there is a method for getting them or not...
>> >
>> > You could use mdvel (velocity) values with atomic masses.
>> >
>> > Bill
>> >
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Apr 15 2011 - 07:00:02 PDT
