*Hi Aadarsh,*
Thanks for sharing this — I’ve actually encountered a similar issue in my
QM/MM umbrella sampling simulations after shifting to a newer AMBER version.
In my case, I noticed that the collective variable started drifting away
from the window center in some windows. Increasing the force constant
helped re-center the sampling around the defined CV value, but ideally, for
a well-defined window and CV range, the system should naturally oscillate
around the window center.
I’m also curious to understand why this behavior might have changed in
Amber24 — if anyone has insights into what could be causing this CV drift
or knows of any relevant changes in the NFE implementation between
versions, I’d really appreciate your thoughts.
Thanks
On Sun, Jul 20, 2025 at 12:32 AM <amber-request.ambermd.org> wrote:
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> Today's Topics:
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> 1. Differences in Umbrella Sampling between Amber18 and Amber24
> (Aadarsh Raghunathan)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Sat, 19 Jul 2025 16:57:28 +0000
> From: Aadarsh Raghunathan <aadarsh.raghunathan.research.iiit.ac.in>
> To: "amber.ambermd.org" <amber.ambermd.org>
> Subject: [AMBER] Differences in Umbrella Sampling between Amber18 and
> Amber24
> Message-ID:
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> PNZP287MB41083AC9843B2B946224DF59E291A.PNZP287MB4108.INDP287.PROD.OUTLOOK.COM
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> Content-Type: text/plain; charset="iso-8859-1"
>
> 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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--
Kriti Shukla
Research Scholar
Department of Chemistry
Indian Institute of Technology, Kharagpur
India. 721302
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Received on Mon Jul 21 2025 - 22:00:02 PDT
