[gmx-users] ndx file with frames

Dan Gil dan.gil9973 at gmail.com
Wed Aug 1 01:41:49 CEST 2018


I have used gmx select to create groups of atoms for each time frame - the
indices of the atoms in each group changed with each step. Then I used this
output in other gromacs utilities such as gmx rdf.

I haven't used plumed, but from your question I believe gmx select might be
a good start for you.


On Mon, Jul 30, 2018 at 9:29 AM, Stefano Guglielmo <
stefano.guglielmo at unito.it> wrote:

> Dear all,
> I would like to generate an index file containing frame numbers selected
> according to a parameter contained in plumed output; I could select the
> desired frames from the output using any scripting/text manipulating tool,
> but I was wondering which should be the suitable format to be read by,
> let's say, trjconv.
> Does anyone have any suggestions?
> Thanks in advance
> Stefano
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