[gmx-users] how can I exclude the solvent from the output?

Athina Meletiou enxam16 at nottingham.ac.uk
Tue Jan 28 19:02:10 CET 2014


I am interested in running a simulation of a mycolic acid; the solvent is water.

However, I need to exclude the solvent from being written in the output in order to reduce the data volume.

So, after using editconf and genbox, what I did was edit the mdp file and add the following lines on the 'output control options' section:

; This selects the subset of atoms for the xtc file. You can =
; select multiple groups. By default all atoms will be written. =
xtc-grps                 = MEO
; Selection of energy groups
energygrps               = MEO

I ran grompp using the input as described above. Then I did an energy minimization with mdrun, but the output I got still contains the solvent.

So obviously I did something wrong. Unfortunately searching the web didn't provide me with any answers, I know I need to edit the lines mentioned above but I am not sure how to actually edit them.

Thank you so much in advance!

Best regards

Athina Meletiou
Department of Chemical and Environmental Engineering
University of Nottingham
University Park
Email: enxam16 at nottingham.ac.uk<mailto:enxam16 at nottingham.ac.uk>

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