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

[Athina Meletiou]

Hello!

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


Athina Meletiou
Department of Chemical and Environmental Engineering
University of Nottingham
University Park
NG7 2RD
Email: enxam16 at nottingham.ac.uk<mailto:enxam16 at nottingham.ac.uk>





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