Re: [AMBER] Can imin=5 of sander treat NPT trajectories properly?

From: Thomas Cheatham via AMBER <>
Date: Mon, 9 Jan 2023 03:37:07 +0000

imin=5 is just post-processing ... the blow-up likely happened in your production MD. Usually a large blow up happens due to overlapping atoms. It is unlikely due to the causes you suggest (lack of correct PBC or solvent overlap). Look at your mdout files from the original MD and/or visualize the trajectories. If you cannot decipher, likely you will need to share the files (topo, mdout, trajectory, mdin) so someone on the list can inspect.


From: Mei Kevin via AMBER <>
Sent: Sunday, January 8, 2023 8:22 PM
Subject: [AMBER] Can imin=5 of sander treat NPT trajectories properly?

Dear all,

I'm trying to analyze energies along some NPT trajectories using imin=5 of sander. Each of these trajectories contains 5000 frames. However, I'm aware that as the analysis goes along the trajectory, the vdW energy increases sharply and abnormally, from ~10000 to ************* in hundreds of frames. I suspect that sander cannot treat periodic box dimension changes properly, so solvent molecules begin to overlap after some time, leading to huge vdW energy. Is that correct and if it is, can anyone give some advice on other solutions?

Much thanks!

mdin file:
    imin=5, maxcyc=1, cut=9.0, ntb=1, ioutfm=1,
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Received on Sun Jan 08 2023 - 20:00:03 PST
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