[gmx-users] How to create a spherocylindrical wall

Jagannath Mondal jmondal.backup at gmail.com
Fri Sep 11 08:27:37 CEST 2015

  I would like to perform a simulation ( without any periodic boundary
condition) where I need to have a wall of spherocylindrical geometry. In
other words the particles will be confined inside a spherocylinder.

 Is there any good suggestion on how to achieve that in gromacs?

1) One option I thought of achieving that is by having a spherocylindrical
wall potential.  Is there a way of putting the wall potential in the form
of a table-potential ? (Not sure cylinder option in gromacs umbrella
sampling  not going to be helpful).

2)  Or,should I put a bunch of hard sphere which constitute the
spherocylindrical boundary so that the particles inside the spherocylinder
will have a repulsive interaction each time they come towards the boundary ?


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