[gmx-users] long-stick molecule solvation
xy21hb at 163.com
Wed Nov 4 00:33:52 CET 2015
Thanks for the reply. However, my system is just a long finite protein with its length of 220 A.
Any further suggestion would be appreciated.
At 2015-11-04 06:13:11, "Justin Lemkul" <jalemkul at vt.edu> wrote:
>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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