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

From: Mei Kevin via AMBER <>
Date: Mon, 9 Jan 2023 03:55:07 +0000

Hi Matthew and others,

I have already done my production run, and it terminated normally without blowing up (I have checked the mdout and restrt). Now I'm just using imin=5 to analyze its mdcrd. Actually I've tried another method: spliting all 5000 frames into 5000 restrt files and analyzing them using a batched sander. Using this method, vdW and total energies of all frames seemed normal. However, this method is very time- and space-consuming, so I wish to do analysis in a more convenient way, but imin=5 seems problematic.

What made me suspicious is that the AMBER manual says "sander sets up parameters for PME from the box coordinates in the initial coordinates input file" in the imin=5 decription. So I guess sander just reads box dimension from the inpcrd file, and it won't be changed in proceeding analysis, even if it is actually changed in the trajectory.

Hi Kevein,

Im not sure whats going wrong, but depending on what you want to compute, you can try the energy, esander, pairwise, or LIE keywords in CPPTRAJ.


> On Jan 8, 2023, at 10:22 PM, Mei Kevin via AMBER <> wrote:
> *Message sent from a system outside of UConn.*
> 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:
> &cntrl
> imin=5, maxcyc=1, cut=9.0, ntb=1, ioutfm=1,
> /
> _______________________________________________
> AMBER mailing list

AMBER mailing list
Received on Sun Jan 08 2023 - 20:00:04 PST
Custom Search