Hello,
I am currently performing umbrella sampling simulations on a DNA-protein complex using the NFE method (infe=1), and have recently shifted from Amber18 to Amber24 for these calculations. However, after updating to the newer Amber version, I am getting significantly different results from my previous simulations.
In particular, in Amber24, the collective variable (CV) appears to drift away from its window center, whereas in Amber18, the CV oscillated around the intended window center, as expected in standard umbrella sampling.
I've gone through the manuals for both Amber18 and Amber24 but could not identify any changes that might explain this behavior, and would really appreciate any suggestions on how to debug my current simulations. I have attached my input script and collective variable definition and am running these simulations with pmemd.cuda.
Thanks a lot for your time and assistance,
Best regards,
Aadarsh Raghunathan
International Institute of Information Technology, Hyderabad
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Received on Sat Jul 19 2025 - 10:30:02 PDT
