From: Jérôme Hénin (jhenin_at_ifr88.cnrs-mrs.fr)
Date: Tue Oct 25 2011 - 02:10:14 CDT
Hasan,
Most of the answers are there:
http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/4125.html
Best,
Jerome
On 25 October 2011 08:28, Hasan haska <hasanhaska_at_yahoo.com> wrote:
> Dear Namd users,
>
> I performed some md simulations for my system adding “velDCDfile” command
> into the conf file. Then I compared the velocity information for the last
> record in .vel ascii file and .pdb file generated from the vel.dcd file if
> velocities are the same. And I realized that velocities of the atoms are
> different in these two files. What is reason for this ? Can you please make
> an explanation about this issue ? In addition to this, when I load vel.dcd
> into psf file and use “pbc wrap –all” command in vmd then save the
> velocities for the last record, I got a another different velocity pdb file
> that has different information. Why these three velocity file has different
> velocity information ? Which velocities should I take into consideration ?
> Please see the attached velocity.dat file.
>
> Thanks for your help.
>
>
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