*
Can I see the tleap script you are running? I'm curious about the water model.
*
If you do tail -n1 <OUTPUT RST7 FILE> , do you get the same box size in all cases?
*
If you run NVT on the output systems, do you get the same starting density?
The coordinates for the pre-equilibrated water molecules are at `amber/dat/leap/lib/`, and I don't see any change on files like 'tip3pbox.off'.
The other factor that may affect the final result is the usage of the keyword "aniso", that prevents tleap from centering and reorienting the solute before adding the box. This increases the box size for a given buffer length.
Best,
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AMBER Mailing List Digest
Today's Topics:
1. solvateoct behavior in Amber26 (Baker, Joseph)
----------------------------------------------------------------------
Message: 1
Date: Tue, 16 Jun 2026 14:55:03 -0400
From: "Baker, Joseph" <bakerj.tcnj.edu>
To: AMBER Mailing List <amber.ambermd.org>
Subject: [AMBER] solvateoct behavior in Amber26
Message-ID:
<CAA5VDpDSCstP8vGa_cQ3Nj9eWtZCx3vpwkNSvTuWcxJsukYpTw.mail.gmail.com>
Content-Type: text/plain; charset="UTF-8"
Hello,
One of my students noticed that their simulations were running much more
slowly suddenly, and when looking at our tleap output we observed that the
solvateoct command seems to be adding a significantly larger number of
water molecules to the system than it has in the past (with the same
padding value, using the same initial structure). We went back and checked
the behavior in 25,24,23,22 versions and they were all consistent with the
number of water molecules being placed by solvateoct. Has there been some
change in the way solvateoct handles building the water shell?
Thanks!
Joe
------
Joseph Baker, PhD
Barbara Meyers Pelson Chair in Faculty-Student Engagement (AY 2024-2027)
Professor, Department of Chemistry
The College of New Jersey
Ewing, NJ 08628
Chair-elect (2026), Trenton Local Section of the ACS
Chemistry Division Representative (2024-2027), The Council on Undergraduate
Research
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