Dear Amber Users,
I have some questions about running MD on GPU. I finished the simulation
and calculated BFE. But I lost some files so I did the simulation again
using the same starting structure, same parameters and same computers/gpu.
However, I didn't get the same results. Before I got MMPBSA around -50
kcal/mol but now I got around -29 kcal/mol and it is similar to MMGBSA. I
compared the structure derived from the last snapshot, but it is also not
really similar.
I know that repeat MD runs will not get the same exactly results, however,
it should be somehow similar, especially when you use the same computer and
same MD parameters, right? So, I just wonder how can I believe in the
results or something wrong.
Best Regards,
Kanin Wichapong
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Received on Fri Jul 05 2013 - 14:00:02 PDT
