[gmx-users] Making an index file for specific solvent molecules

Aharon Gomez aharongomez at udec.cl
Mon Jan 20 18:08:37 CET 2020


Hi everyone,

I'm working on gas like molecules diffusion in protein. I have an equilibrated system and now I want
to replace solvent molecules with some other molecule, like O2, but i want to select just the water molecules
that are placed over some distance to my protein.
Is there any built in tool in gromacs to make an index file of these solvent molecules or any other way to do it?

Aharon Gomez Llanos
Estudiante de Doctorado en Ciencias c/m en Química
Universidad de Concepción



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