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.
[email protected] http://folding.bmc.uu.se
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