[gmx-users] Reg: Simulating large number of molecules

[David van der Spoel]

On 2010-12-24 11.06, vinothkumar mohanakrishnan wrote:
> Hi all
>
> I want to simulate more than 1000 molecules of say octane r any alkanes
> in gromacs. after doing a little math i find my box dimensions for the
> molecules. but when i use genbox to insert multiple molecules in my
> local system after running some time it says cannot allocate memory but
> when the same command i gave it in a Linux cluster interactively (HPCE)
> it goes well and fills the box with required number of molecules and i
> get the correct density. but even then there are limitations such as i
> can't go beyond 1500 molecules with required box dimensions. So how one
> can about simulating more than 1000 molecules of alkanes r any molecules
> for that matter? I know that this problem doesn.t occur for water. any
> help is highly appreciated.
>
> Regards
> Vinoth
>
genbox is memory hungry. Try using genconf.

-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se