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

[sapna sarupria]

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.

Thank you

Regards
Sapna

On Thu, May 29, 2008 at 4:45 PM, sapna sarupria <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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