Re: [AMBER] dimer shifts under NPT ensemble

From: David A Case <>
Date: Thu, 25 Feb 2021 21:02:24 -0500

On Fri, Feb 26, 2021, Qinghua Liao wrote:
>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.
>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 don't know of any easy way to avoid this problem altogether. Don't use
really strong restraints in NPT steps, to allow the dimer interface to relax
as the box shrinks.
>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.

When you say "it was still the same", do you mean that nothing at all
changed? Using a closeness of 0.75 should increase the initial density,
and hence reduce the amount by which the box needs to shrink. If nothing
changes when you change the closeness parameter, maybe there is something
wrong at the tleap step.

Finally, do you know that the dimer is unstable under your simulations, or
is that just a "worry"?


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Received on Thu Feb 25 2021 - 18:30:02 PST
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