[gmx-users] How can I implement a radial potential field in GROMACS?

Justin Lemkul jalemkul at vt.edu
Tue Aug 1 00:52:46 CEST 2017

On 7/31/17 1:07 PM, Wes Michaels wrote:
> Hello,
> (Cross-post from my original post here: https://www.researchgate.net/post/How_can_I_implement_a_radial_potential_field_in_a_MD_simulation_GROMACS)
> Is there a way to apply a potential field to all atoms in a simulation box in GROMACS? I'd like to implement some radial potential energy function, such as U(r)=k*r^2 or similar, that applies a force to each atom as a function of its position. In my case, I’d like to draw atoms towards the center of the box.
> I looked into implementing this with the pull code with a dummy atom, but I gathered that the pull code acts on the center of mass of the specified index group, not on each atom in the group. So, if all the atoms in my simulation in a given index group are distributed radially around the center of my box, no force will be applied. Scaling behavior of Coulomb and LJ potentials on the dummy atom seems to rule them out as possible sources of a potential, too.
> Is there a way I can modify the reference positions of position restraints of atoms to be centered at the middle of the box, instead of the atom's initial position? Or, can I implement a solution using force switching that acts only on the dummy atom? Or, is there another way to tackle this problem?
> Thanks! Any and all suggestions are appreciated. If clarification is needed on my desired goal, just let me know.

It seems to me that you can do this with a simple use of position restraints on 
all atoms, with a reference position set for each at the middle of the box via 
grompp -r.



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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