[gmx-users] How to create a spherocylindrical wall

jagannath mondal jm3745 at columbia.edu
Mon May 16 07:23:19 CEST 2016

  This dates back to an old query on using restraints to create a
spherocylindrical confinement.

  a) Based on previous suggestions, we were exploring the options of
flatbottomed potential.
   However, it has three options only: sphere, cylinder and layer. We
wanted to create a combination of cylinder and (hemi)sphere to make a
 hollow spherocylinder. But we do not find how to make the hemisphere using
flatbottomed potential.
  Also, we wanted to have the centers of cylinder and sphere in  different
locations. However, we are not sure within the current gromacs
implementation, how we can have two different centers for flat-bottomed

b) In worse case scenario, we were thinking of modifying the source code of
gromacs flat-bottomed restraints to have the option of spherocylindrical
restraints. In that case, can some one point out the relevant locations of
source code for flat-bottomed potential withing gromacs 5.x installation


On Sat, Sep 12, 2015 at 7:52 AM, Barnett, James W <jbarnet4 at tulane.edu>

> 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
> --
> Gromacs Users mailing list
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.

More information about the gromacs.org_gmx-users mailing list