Re: [AMBER] Temperature variation in QM/MM simulation with AMBER18/G09

From: Abhilash J <>
Date: Sat, 25 May 2019 11:23:38 +0530

I already did the equilibration with restraints using MM.
I did minimization (QM/MM) by starting with a small basis and and
increasing it as i went ahead.
I think i will be patient as you suggested.

On Thu, May 23, 2019 at 6:31 PM David A Case <> wrote:

> On Thu, May 23, 2019, Abhilash J wrote:
> >
> > I am trying to do QMMM but somehow the temperature has decreased from
> >300K and sort of stabilized (slightly increasing trend to confess) (i am
> >trying to keep it to 300K). I don't understand why. I am using AMBER 18
> >with gaussian09 interface. I am attaching the temperature graph, complete
> >input file and bit of the output here . I am not getting where i am
> getting
> >it wrong.
> You are looking at the behavior of 0.22 ps of trajectory. It generally
> takes a lot longer than than to equilibrate a thermal system. Setting
> gamma_ln to a larger value will make the temperature closer to the
> target, but it will still take a long time (counting in .002 ps time
> steps) to acheive your goal.
> If at all possible, do an equilibration using MM (probably with restraints
> on the quantum atoms.) Then turn on QM/MM, probably starting with a small
> basis set. But since you have 80+ atoms in your quantum region, and
> are using B3LYP with a large basis, you are going to need a lot of
> patience here.
> ...good luck...dac
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Received on Fri May 24 2019 - 23:00:02 PDT
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