[gmx-users] plot velocity of center of mass

David van der Spoel spoel at xray.bmc.uu.se
Mon Dec 3 09:34:25 CET 2007

Li Qiang wrote:
> Dear all users,
> I want to plot the velocities of center of mass for my peptide. Reading
> from 3.3 manual, there seems to be two ways--g_com and g_traj. 
> However,
> 1, g_com can not be found in /usr/local/gromacs/bin. Is there anything
> missed for my installation?
> 2, $> g_traj -f md.trr -s md.tpr -ov veloc.xvg -com  
> but there is only one line in the output file, i.e. the last frame of my
> trajectory. The same thing happens for "-of force.xvg". but for "-ox
> -coord.xvg" all the times are written out! 
> Is there any physical meaning for this? or something is wrong?
> GROMACS 3.3.1 is used.
the velocities have not been saved. please check mdp file options.
> thank you
> Qiang
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David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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