[gmx-users] Grid statement in md.log

David van der Spoel spoel at xray.bmc.uu.se
Fri May 30 08:25:12 CEST 2008


sapna sarupria wrote:
> Dear All,
> 
>  During simulations of some ions solvated in water
> (where water is constrained using SHAKE) I get the
> statements looking like the following in the md.log
> files:
> Grid: 4 x 4 x 4 cells
> 
> Grid: 5 x 5 x 5 cells
> Grid: 4 x 4 x 4 cells
> Grid: 5 x 5 x 5 cells
> Grid: 4 x 4 x 4 cells
> Grid: 5 x 5 x 5 cells
> Grid: 4 x 4 x 4 cells
> 
> The system consists of 10 ion pairs and water (SPC/E,
> 518 water molecules) and simulations are run in NPT
> 
> ensemble (T=280 K). Can anyone please explain what
> this statement means and if it should be a cause of
> concern. The simulations have run without crashing for
> 25 ns. The simulations were run using gromacs 3.2.
> 
The number of grid cells for neighborsearching. It fluctuates if the 
size of the boz fluctuates due to pressure coupling. This is normal.

> Similar output was found in gromacs 3.3 simulations
> except in this case there is only one ion pair (in 518
> water molecules) which is constrained at a certain
> distance using constraint = all_bonds in run.mdp file.
> 
> 
> Thanks in advance for your response.
> 
> Regards
> Sapna 
> 
> 
> 
> 
> -- 
> Sapna Sarupria
> Ph.D. Student - Chemical Engineering
> Rensselaer Polytechnic Institute
> Troy, New York 12180
> U.S.A.
> Ph#: (518)276-3031
> Life isn't about finding yourself. Life is about creating yourself.
> George Bernard Shaw.
> Dare to Dream
> 
> 
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-- 
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se



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