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

From: David A Case <>
Date: Thu, 23 May 2019 09:00:40 -0400

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 Thu May 23 2019 - 06:30:02 PDT
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