[gmx-users] Re: Re[6]: Using Morse potentials with ENCAD force field

[Andy Shelley]

I am trying to make a radial temperature profile of a given thickness. I
originally used the confout.gro file containing the final output of velocity
and position of each atom to calculate the temperature from the velocity but
would like to take time averages now.

Andy

On Sat, Sep 6, 2008 at 4:21 AM, Vitaly Chaban <chaban at univer.kharkov.ua>wrote:

>
> AS> The system works now, thanks for finding a simple mistake.  Another
> question I had is if I want to calculate the average velocities of all the
> atoms over a period of time can I use g_traj to create an average velocity
> of the atoms, but looking at all_veloc.xvg file the atom number starts at 0
> so I don't know where to cross reference it with another file to coordinates
> of that atom.  Is there a function in GROMACS that will give averages of
> velocities and positions of atoms?
>
> AS>
>
>
> I think you can find the average atom velocity from of temperature of the
> system. Telling the truth I don't know why you want ones. If you tell the
> final result you need probably I can be of more use.
>
>
> I don't really remember from what number the atoms numbering starts in the
> programme you speak about but if it starts from zero this corresponds to the
> first atom in your conf.gro.
>
>
> AS> Thanks,
>
> AS> Andy
>
>
>
>
>
>
>
> --
>
> Vitaly V. Chaban
>
> School of Chemistry
>
> National University of Kharkiv
>
> Svoboda sq.,4, Kharkiv 61077, Ukraine
>
> email: chaban at univer.kharkov.ua
>
> skype: vvchaban
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20080908/e659c67b/attachment.html>