[gmx-users] Flat-bottom spherical potential

Justin Lemkul jalemkul at vt.edu
Wed Jul 5 15:06:45 CEST 2017

On 7/5/17 8:36 AM, Shraddha Parate wrote:
> Hello all,
> I had emailed to Gromacs Users List the following query as per the attached
> thread (https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-
> users/2017-June/114166.html)
> Justin mentioned about applying a flat-bottom spherical potential which
> will keep the droplet formed on the surface. I tried my best to figure out
> the corresponding file to implement the potential, but could not find. Can
> anyone please let me know more clearly on how I can make this kind of
> changes?

The origin of the potential is at the center of the sphere.  You would apply a 
flat-bottom restraint to the water oxygens by assigning a suitable spherical 
restraint and a radius that you want (see the manual).  Then, you need to 
generate a "fake" coordinate file that sets the (x,y,z) coordinates of each 
water O atom to the center of the sphere and pass this coordinate file to grompp 
-r.  This sets the origin of the restraint, so that the radius you want is enforced.



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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