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

From: Petr Kulhanek via AMBER <>
Date: Tue, 10 Jan 2023 08:20:00 +0100

Dear Kevin,

> 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?

> &cntrl
> imin=5, maxcyc=1, cut=9.0, ntb=1, ioutfm=1,

for the NTP condition, you have to use ntb=2. With ntb=1 (constant
volume), I assume that sander reads the box info from a coordinate
file, which might deviate significantly from your production
trajectory data.

Best regards

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#  Petr Kulhanek
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Received on Mon Jan 09 2023 - 23:30:02 PST
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