Re: [AMBER] dimer shifts under NPT ensemble

From: Qinghua Liao <>
Date: Fri, 26 Feb 2021 08:31:16 +0100

Dear David,

Thanks very much for your reply!

On 2/26/21 3:02 AM, David A Case wrote:
> 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.
Normally, I do not use such a high positional restraints during
equilibration, it is just a test
to see it will work or not.
>> 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"?
When I used a closeness of 0.75 angstrom, I still see a shrink of ~2
angstrom on each dimension,
and there is still a shift of the dimer.

Yeah, it is my worry about an unstable dimer, but actually it is stable,
as I think new interaction network
might be formed at the interface to stabilize the dimer. I don't know
whether it has an influence or not, but it is better to
not have a shift of the dimer. Thanks!

All the best,

> ....dac
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Received on Fri Feb 26 2021 - 01:00:02 PST
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