[gmx-users] Combining various Flat-bottomed Potentials

Justin Lemkul jalemkul at vt.edu
Wed May 25 13:08:40 CEST 2016

On 5/25/16 1:44 AM, jagannath mondal wrote:
> Hi
>   I am also interested in the issue of using a  flat-bottomed restraint,
> for a spherocylinder.
>  However, I am not sure whether the current gromacs settings of even a
> linear combination of a sphere and cylinder can help here to generate a
> spherocylinder.
> If we put the spherical and cylindrical restraint on the same particle
> (under the [position restraints] flag as Justin and Chris has suggested ),
> the particle will be either be in a spherical confinement or in a
> cylindrical confinement .  But for a spherocylinder, we need two
> hemispheres which are capped on the two ends of a cylinder.
> Hence, for a spherocylindrical restraint, what is needed here is a
> restraint which will restrain the particle on going out when the z
> coordinate of the particle exceeds the diameter of the cylinder AND the
> sqrt(x**2+y**2) of the particle exceeds the length of the cylinder.
> I am wondering whether this is possible within the current gromacs
> implentation.
> If it is not, I was interested in editing the source code relevant for flat
> bottomed potential, to implement it for a spherocylinder. Is the following
> path within gromacs directory right place to make the changes ?
>   gromacs-5.0.6/src/gromacs/gmxlib/bondfree.c

Yes, it is.

You basically need to create a hemisphere mode.  The cylinder restraint does not 
act parallel to the cylinder axis, so the restraint at the ends just needs to be 
enforced by the hemisphere.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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