Re: [AMBER] Temperature and TI with qm/mm

From: case <>
Date: Sat, 9 Nov 2013 10:25:45 -0500

On Sat, Nov 09, 2013, Fabrício Bracht wrote:

> The problem is
> that the temperature of the system falls from the previous 298K to around
> 213 K and it stays like that for as long as I have simulated.

This looks like a problem with SHAKE inputs: you are shaking the MM bonds
involving hydrogen, but have set qmshake=0, which turns off shake in the
quantum region. I'm guessing that the code is computing the number of
degrees of freedom assuming shake is turned on, and is not correcting that
number when it processes the qmshake=0 input.

Try adjusting either qmshake or the noshakemask variables so that you are
doing the same amount of SHAKEing in both qm and mm calculations. (Simplest
is to use the default value for qmshake, which should be OK unless bonds to
hydrogen are being made or broken.)

...good luck...dac

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Received on Sat Nov 09 2013 - 07:30:02 PST
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