[gmx-users] gmx dipoles with dynamic indices (gromacs 5.0.x)

Daskalakis Vangelis vdas.pilot at gmail.com
Wed Sep 16 00:13:55 CEST 2015

I want to use a dynamic selection scheme (select different atoms based on
the same selection criteria for each frame of a trajectory) and pass this
selection/ info to the gmx dipoles tool. It seems that the -select option
cannot be used.
I tried to use dynamic selection through gmx select. The gmx select output
(using the -on option, e.g an index.ndx file) was indeed a correct
selection of the molecules/ atoms within the system for each frame,
resulting in a large index.ndx file for the whole trajectory.
When I use the -n index.ndx option for the gmx dipoles, there is of course
this huge list of groups of atoms (one group per frame) showing up. I
cannot choose just one frame selection group, as I want the gmx dipoles
tool to process each frame based on the selected group of atoms for each
frame written in index.ndx by gmx select.
Any ideas or suggestions? Thank you.

* <http://www.cut.ac.cy/est/staff/evangelos.daskalakis/>*


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