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

From: Mei Kevin via AMBER <amber.ambermd.org>
Date: Mon, 9 Jan 2023 03:22:24 +0000

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,
AMBER mailing list
Received on Sun Jan 08 2023 - 19:30:02 PST
Custom Search