Hi,
Zeroing some charges won't help. Actually, the QM zone charges are
already zeroed before the QM calculation. I believe your best bet here
is postprocessing, i.e., write a small program to get the charges from
the prmtop file and the structure from the mdcrd or restrt (depending
on what you want) and calculating the interaction yourself. If you
need the QM charges, you'll have to print them and adjust the program
to use the correct charges, since the charges on the prmtop are the
RESP charges, not the QM charges, which can be different in every
step.
Good luck,
Gustavo Seabra
Professor Adjunto
Departamento de Química Fundamental
Universidade Federal de Pernambuco
Fone: +55-81-2126-7417
On Mon, Oct 10, 2011 at 4:44 PM, Yao Yao <yao0o.ymail.com> wrote:
> 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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>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
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Received on Tue Oct 11 2011 - 11:30:03 PDT
