[gmx-users] long-stick molecule solvation

Justin Lemkul jalemkul at vt.edu
Tue Nov 3 23:13:23 CET 2015

On 11/3/15 9:57 AM, xy21hb wrote:
> Dear all,
> I have a long-stick "carbon-nanotube" like protein to solvate with its length of ~ 220 A and diameter of 50 A.

Does this imply that you have connectivity across PBC, like an "infinite" nanotube?

> I tried using a triclinic box with the longest box axis aligned to the C-alpha of the protein, and the protein seems to be properly solvated.
> However, energy minimization with GROMACS 5.0 shows,
> "There is no domain decomposition for 48 ranks that is compatible with the given box and a minimum cell size of 9.59877 nm"
> Any suggestions on that?

If the answer to the above question is "yes," then you need "periodic_molecules 
= yes" in your .mdp file.



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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