Hi Qiantao,
Thanks for your help. I guess you may have extensive experience in the similar calculations.
Just for curiosity, since the interaction between the QM and MM is mutual, would it be also fine and more convenient if I zero the QM charge? And can I zero specific residues' charge to get their interaction energy? All I need is just electrostatic interaction energy between two specific groups in the system, they are not necessarily the QM and MM, respectively.
Many thanks,
Yao Yao
________________________________
From: Qiantao Wang <qiantao.wang.gmail.com>
To: Yao Yao <yao0o.ymail.com>; AMBER Mailing List <amber.ambermd.org>
Sent: Friday, October 7, 2011 1:17 PM
Subject: Re: [AMBER] Interaction Energy in QMMMMD
Hi Yao,
As far as I know, current Amber doesn't have this kind of facility (?)
If you are only interested with the electrostatic QM/MM interaction
energy, one simple way you could try is to modify the prmtop file by
zero the charge of the atoms within the MM part that you are
interested in. Then calculating the QM/MM interaction energy with the
original prmtop and with the modified prmtop file separately. The
difference between two interaction energy will be the contribution
(approximately) of the zero charged MM part.
Or, if you don't mind to tweak the source code a little bit. You can
first save the converged density matrix with original prmtop file.
Then do the second calculation with the saved density matrix after
zero the charges. This way, from my personal experience, you may get
better result.
Best,
Qiantao
On Fri, Oct 7, 2011 at 3:27 PM, Yao Yao <yao0o.ymail.com> wrote:
> Hi,
>
> I am running a QMMMMD simulation. For some reason, I wanna check the interaction energy between different parts
>
> of my system, like solutes and solvent, or QM part and MM part. Is there any way to do this in Amber?
>
> Thanks,
>
> Yao
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>
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Received on Mon Oct 10 2011 - 13:00:04 PDT
