[gmx-users] How to create a spherocylindrical wall

[Barnett, James W]

On Fri, 2015-09-11 at 11:57 +0530, Jagannath Mondal wrote:
> Hi
>   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).

This might be do-able and would not require a table potential. Check
out flat-bottom restraints in section 4.3.2 in the reference (PDF)
manual.

> 
> 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 ?

I'm not sure how you would implement this in a simple way with GROMACS.


-- 
James “Wes” Barnett, Ph.D. Candidate
Louisiana Board of Regents Fellow

Chemical and Biomolecular Engineering
Tulane University
341-B Lindy Boggs Center for Energy and Biotechnology
6823 St. Charles Ave
New Orleans, Louisiana 70118-5674
jbarnet4 at tulane.ed