AMBER Archive (2008)

Subject: AMBER: Gbsa in NAB

From: Hu, Shaowen (JSC-SK)[USRA] (Shaowen.Hu-1_at_nasa.gov)
Date: Thu Apr 10 2008 - 12:04:14 CDT

Dear Dr. Case,

Thank you very much for your help. I am doing some tests on NAB with a
section of DNA. I found, if I turned on gbsa, the structures of DNA are
very distorted during the trajectories, but if I set gbsa=0, the
trajectories are good comparing to Sander calculation. I have tried
three GB models, two force fields(ff99SB and ff99bsc0), and various cuts
and heat baths.
It seems that gbsa in NAB does not behave as good as in Sander.

Please do some tests or examine your code if you are interested.

All the best,
Shaowen
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