Hello,
I have faced the same issue while doing US for a RNA-Protein system in
Amber24 (Not tried with Amber18). But by changing the anchor position or
width of sampling to : .5, 10.5, 10.5, 20.5 (as in your case giving a 10
difference) and increasing anchor strength to 7.5 and 10. ( Even though
gave somewhat sharp histogram ) obtained the window almost near ( 1-2
angstrom difference still is there) the window center. Hope this will be
helpful to you. Feel free to ask if any queries are there.
Regards
Sidharth.E.K.
PhD Scholar
NACB Lab
Chemistry Department
IIT Bombay
On 2025-07-19 22:27, Aadarsh Raghunathan via AMBER wrote:
> 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 Mon Jul 21 2025 - 22:30:02 PDT
