[gmx-users] Filling box with long linear molecules

Kamps, M. m.kamps at student.rug.nl
Mon Apr 24 10:46:27 CEST 2017

Dear GMX users,

I am working with polymers (~20 carbon atoms) in an enclosed box. In
order to fill this box with polymers, I currently use an iteration of
multiple steps.

Currently, the polymers are created via an external code, and the
resulting polymers are linear strings of polymers, with only a
'zig-zag' motion at the carbon atoms. Currently I am filling this box
via the 'gmx insert-molecules -nmol X' command, where it will try to
fill the box.

Due to the orientation of the polymers, the box is considered full and
GROMACS cannot add any more polymers. However, after performing a
small relaxation the polymers will 'bend and twist' all around each
other, resulting in lots of empty space. This process is repeated
several times until gmx insert-molecules can no longer fit any more
polymers in the box.

My question, is there a more efficient way to do this? Can GROMACS
insert-molecules while 'bending' the polymers?

Kind regards,


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