[gmx-users] Re: Grid statement in md.log

[David van der Spoel]

sapna sarupria wrote:
> Hello David,
> 
> Thanks a lot for your response.  My major concern is that this statement 
> does not show up as often  in most of the simulations but in some it 
> shows up like illustrated below* (continuously). For example, it does 
> not show up in protein+water simulations but does comes up in ion+water 
> simulations continuously (both are NPT simulations therefore the box 
> volume fluctuates in both cases)
> 
> *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
> 
> 
>  Is there a particular reason for this? From my observation, it appears 
> that the frequency of this statement is independent of the frequency 
> with which the md.log is written.
> 
Typical neighborsearching frequency is 5 steps, so it could be that 
often. We could take it out actually, it was put in long time ago to 
debug exploding systems or something along those lines.

> Thank you
> 
> Regards
> Sapna
> 
> On Thu, May 29, 2008 at 4:45 PM, sapna sarupria 
> <sapna.sarupria at gmail.com <mailto:sapna.sarupria at gmail.com>> 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.
> 
> 
>     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 
> 
> 
> 
> 
> -- 
> 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