Thanks for the suggestions, it made things clearer.
ulimit was set to unlimited on my machine and some of the arrays with the extra points are already allocated on the heap in the original version of the code. Plus, for my test run I just have 18 TIP5P waters and one CH3SH with 6 extra points on sulfur, which I guess should not overflow the stack...
I also spotted a few places in the code where if statement directly checks for two or one extra points and then does something. May be this has some effect as well.
Anyway, I think it is not a wise idea to mess around with the source code. So, I need to explore other options such as OpenMM or mdgx (btw, thanks for bringing it, I didn’t know that Amber has this package).
Best,
Max
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Received on Tue Mar 01 2016 - 19:00:03 PST
