[AMBER] dimer shifts under NPT ensemble

From: Qinghua Liao <scorpio.liao.gmail.com>
Date: Fri, 26 Feb 2021 01:04:23 +0100


I am using Amber 20 so simulate a homodimer, I followed the general
protocol, minimization, NVT heating, NPT equilibration, and then NPT
production run.
However, I found that the two monomers of the homodimer got a little
closer (~0.5 angstrom) when I started the NPT equilibration, even I
applied positional
restraints on all heavy atoms with a force constant of 500 kcal/mol A2.
With such a high positional restraints, I did not see a shift back of
the two monomers,
but the system got used to the shift of high positional restraints due
to the shrinking of the homodimer.

My understanding is that when the ensemble switched from NVT (heating)
to NPT (equilibration), the volume of the water box shrinked,
which pushed the two monomers getting closer. I checked the box
dimensions, each dimension shrinked by 2 angstrom. I made a figure of it:
(blue: NVT, red: right after switching to NPT)

Even though the shift is just a little, I am still worried that this
shift could still somehow mess up the interactions at the interface,
leading to a relatively unstable dimer.

I was thinking of using NVT ensemble for every step, but I also learned
that a NPT equilibration is still necessary.
I also tried to reduce the closeness of waters (0.75 angstrom) when
generating the topology and coordinate files, as it could add more water,
and the water box might shrink less when switching from NVT to NPT
ensembles. But it was still the same.

Any comments and suggestions are welcome and appreciated!

All the best,

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Received on Thu Feb 25 2021 - 16:30:02 PST
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