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

From: Carlos Simmerling via AMBER <>
Date: Mon, 9 Jan 2023 09:45:23 -0400

This should not be a problem. The issue could be in the details.
-was the trajectory processed at all before imin=5?
-does the input file match the energy flags etc from the MD?
-does the prmtop match the MD?
-are the energies for the first few frames roughly the same as in the
original md output? (they likely won't match exactly since the snapshots
are typically written at a different step than the energy info during md)
Also I suggest using the same inpcrd for this sander run as was used for
the MD (to get the best pme setup match).

On Sun, Jan 8, 2023, 11:55 PM Mei Kevin via AMBER <> wrote:

> 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,
> I’m not sure what’s going wrong, but depending on what you want to
> compute, you can try the energy, esander, pairwise, or LIE keywords in
> Best,
> Matthew
> > 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
> >
> >
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Received on Mon Jan 09 2023 - 06:00:03 PST
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