[gmx-users] Simulation runs on iMac but explodes on cluster

Luke Goodsell luke.goodsell at gmail.com
Wed Jul 13 10:46:30 CEST 2011

Hi Emanuel,

What kind of compounds are you simulating?****
> ~1800 atom protein

> What size of box are you using?
Not sure of specifics, since the tpr file was provided by a collaborator,
but it appears to be ~ 7nm in each dimension

> ****
> Do  you run on multiple thread when you run it on your iMac?
No. Compiled with --disable-threads

> ****
> How many CPU’s are you using on the cluster?
1. Compiled with --disable-threads

I'm not so much interested in diagnosing what caused the LINCS failure as
I've spent a lot of time trying that already. I'm more concerned about what
is the difference between the two environments that leads to such a failure.
That one produces a stable simulation and one so stubbornly refuses to work
implies a pretty significant difference.

What can I change to try to identify the cause of this discrepancy?

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