[gmx-users] Unexpected behavior in the output of gmx insert-molecules using the -ip option.

Abhishek Acharya abhi117acharya at gmail.com
Tue May 30 05:11:31 CEST 2017

Dear GROMACS users,

I want to insert my molecule of interest in a simulation box at specific
positions, specified by a dat file.

Now, when I run insert-molecules, I find that on "certain occasions" (yes,
it doesn't happen always.), the program also inserts the molecule
at the origin [0 0 0]. It seems that it is appending the input coordinates
of my molecule, provided with -ci,
to the final coordinate file, something which should not happen.

Is this behavior known? Of course, it is trivial to remove the extra
coordinates, but it becomes an effort if a large number of systems need to

Thank you.

Abhishek Acharya
Research Associate,
Department of Molecular Nutrition
CSIR-Central Food Technological Research Institute,

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