[gmx-users] Visualizing hexamer with solvent

Simone Orioli simone.orioli at unitn.it
Thu Jun 27 08:51:36 CEST 2019

Hello everyone,
I'm simulating a hexamer and I would like to visualize it together with
solvent (to see if the core of the complex is getting hydrated). However,
all my attempts with trjconv have been unsuccessful. I know that in
principle one should do the following

gmx trjconv -f md.trr -s md.tpr -pbc mol -ur compact -center -o centered.xtc

but I'm not sure which group I have to choose for centering. I read online
that it should be only one of the chains, but if I try to pass an index
file with -n, trjconv automatically assumes I want to use the same indices
for both centering and output, which is not the case. What am I doing wrong?

Thank you for your help!

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