On 24/12/2010 9:06 PM, 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.
OK, so I think you've demonstrated that your Linux cluster nodes have
more memory available.
> but even then there are limitations such as i can't go beyond 1500
> molecules with required box dimensions.
Read genbox -h. Molecules get placed randomly at interstices. Close
packings are intrinsically non-random, so you won't get them from random
packing.
> 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.
If you want more molecules, use a bigger box. If you want more molecules
at high density, use a bigger box and very careful, very gentle pressure
coupling to compress it.
Mark
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