[gmx-users] No DD grid found

Justin A. Lemkul jalemkul at vt.edu
Mon Mar 28 14:17:50 CEST 2011

André Ferreira wrote:
> Dear all,
> I am having some problems with some molecules that I am currently 
> simulating. I got simulation box that is constituted by 100 oligomer 
> molecules (190 atoms each), in a cubic box with 7 nm side (50K). Since 
> the molecule is quite long I am using a rcoulomb of 2.8 nm and rvdw of 
> 3.4 nm. When I try to perform the simulation mdrun can't find DD grid 
> for more than 48 cores, which is a huge handicap. This is the first time 
> that I am working with longer molecules, and I never had this problem.

The DD grid is established based on cutoffs, constraints, and several other 
criteria.  I would say that ad hoc changes to the cutoffs are causing your 
problems.  The settings for rcoulomb, rvdw, and rlist are not dependent upon the 
contents of the system, rather the force field you've chosen.  Elongating them 
beyond what the force field prescribes often leads to nasty artifacts.  Using 
more sensible values for these parameters will probably fix everything 
DD-related, as well as lead to reliable trajectories.


> Really appreciate the help,
> André


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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