Heya,
Take a look at the post I made a while ago at the 3rd party tools section of this forum. mdvwhole will solve your problem and you do not need to fiddle with your trajectory. I do on know how you solvent is named, but after installing (takes a while as I did not clean the dependencies yet…) you should run the following command replacing WATER and IONS with their respective residue names in your system:
mdvwhole -f your_gro_file.gro -x your_xtc_file.xtc -sel ‘not resname WATER IONS’ -o whole.xtc
as the output will not include the solvent and ions, you will also need to run this command once to create a matching gro file (if you want to visualize).
mdvwhole -f your_gro_file.gro -x your_gro_file.gro -sel ‘not resname WATER IONS’ -o whole.gro
Please contact me if you have any issues and/or create an issue at the github page.
Cheers,
Bart