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Bug #107

-ng option to g_traj has no effect

Added by Jonathan Moore about 13 years ago. Updated about 13 years ago.

Status:
Closed
Priority:
High
Category:
analysis tools
Target version:
Affected version - extra info:
Affected version:
Difficulty:
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Description

Regardless of what I set for the -ng option for g_traj, it only asks me for one
group.

History

#1 Updated by David van der Spoel about 13 years ago

This option depends on other flags, in particular -com and -mol. Please give a
full command line.

#2 Updated by Jonathan Moore about 13 years ago

If -ng is intended only to be used with -mol or -com (I didn't see that in the
documentation), then I guess it isn't a bug. Like the poster on the mailing
list today, I was trying to use g_traj to output the coordinates as a function
of time for several different groups. I wanted to use the -ng option so that I
could choose those various groups during one run of g_traj (like I did with the
-ng option for g_mindist). I didn't want c.o.m. coordinates or molecular info,
so I didn't use -com or -mol with -ng. Anyway, I ended up putting all of the
groups of interest in a single group and also using trjconv to get the coordinates.

#3 Updated by David van der Spoel about 13 years ago

Do you mean you want all the coordinates of all atoms in a number of groups?
I could imagine plotting the c.o.m. coordinates for a number of groups, which
could also be (ab)used for plotting atom-coordinates for many atoms, by making
one-atom groups.

#4 Updated by Jonathan Moore about 13 years ago

Yes, I wanted all coordinates for all atoms in a few groups (not to plot
them) to use to calculate a property for which a GROMACS tool isn't available
(local water diffusion coefficient as a function of distance from the solute).
Making one-atom groups is in fact what I did because I needed the positions of
all waters as a function of time. Anyway, I realized that I could use trjconv
instead and output as a gro that I could then post-process.

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