[gmx-users] gmx solvate

Alexander Alexander alexanderwien2k at gmail.com
Tue May 10 20:09:24 CEST 2016

Dear gromacs user,

As you know, the "gmx solvate" can be used as below to merge two gro files
which have an identical box size;

gmx solvate -cp A.gro -cs BC.gro -o ABC.gro

The A.gro contains only the "A" molecules serving as solute while BC.gro
contains two types of B and C molecules serving as the solvent.

Usually, some of the solvent atoms are removed (either B or C or both of
them) from the final ABC.gro file because of overlapping.
My question is that how I can  enforce the program to remove only from one
of the species (for example, B , not from C) if something want to be


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