Hello,
As far as I know, there is no way of getting the velocities in ptraj. You
can write a script or just do some copy-paste from the old restart to the
new one to get the velocity information in there.
Hope that helps,
Jason
On Thu, Aug 19, 2010 at 2:24 AM, manikanthan bhavaraju <
manikanthanbhavaraju.gmail.com> wrote:
> Dear all,
> Currently I am using amber8 to calculate the binding energies using TI.
> During the first step while making the atomic charges zero using TI, for
> the substrate molecule (explicit solvent model) at clambda=0.70292, I ran
> the simulations for 19 ns. At the 19th ns the rst file corrupted as a
> result
> I am unable to submit the previous .rst file for next simulation. On
> visualization in VMD I have observed some of the hydrogen molecules has
> diffused some what out of the box. I have reimaged them back into the box
> using ptraj, but this gives only reimaged residues with new coordinates.
> But I am trying to reimage all the residues with new velocities using
> ptraj
> and I have used the following script.
>
> trajin sub.rst
> trajout sub_reimage.rst restart
> center :1-1
> image center familiar
> go
>
> 1 is the substrate molecule. But the new .rst file generated by ptraj has
> coordinated but has 0.0000 for the velocities. How can I get new velocities
> using ptraj. Any help is really appreciated.
> I have also tired iwrap=1, but it didn't work.
>
> manikanthan
>
> --
> Manikanthan Bhavaraju
> Graduate Teaching Assistant
> Dept. of Chemistry
> Mississippi State University
> office no : 662-325-4633
> MS -39762
> USA.
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Aug 19 2010 - 07:30:04 PDT
