[gmx-users] query on implementation details of flat-bottomed potential

Jagannath Mondal jmondal.backup at gmail.com
Mon May 23 06:48:20 CEST 2016

  I have to impose a  spherocylindrical confinement on the particles I am
 currently performing simulation with.
For that I will appreciate your feedback/comments regarding two of my plans:

1.  I was mainly looking at flat-bottomed potential option within gromacs
to see if it can be used to implement a spherocylindrical confinement.
However, the current implementation of gromacs works with either for sphere
or cylinder. But it is  not implemented for spherocylinder. I was wondering
whether it is possible to create a combination of both of the existing
flatbottomed potential to obtain a spherocylindrical potential.

 If the current gromacs implementation does not allow us to create a
spherocylindrical flat-bottomed potential, can someone point out the
location of relevant source code in gromacs directory where the
flat-bottomed potential is implemented ? I could then modify the source
code for a spherocylindrical geometry.

2. I was also thinking of alternative way of incorporating
spherocylindrical confinement by adding a table potential. But my question
is that one needs to define an energy group which will be interacting by
this table potential. But the spherocylindrical geometry does not have any
particle in boundary. In that case, how  can one proceed?

Your response will be appreciated.

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