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

[vinothkumar mohanakrishnan]

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
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