Dear Ross, dear Andreas! Could you be so kind to answer my question
associated with the topic!
As I suppose, it is not relevant to use TOTAL potential energy of
complex protein-solvent QM/MM system (where QM is the active site) to
compare two different energy states of the active site, because
motions in regions distant to the active site may significantly affect
the energy profile.
So, is it reasonable in this case to use just DFTBESCF energies to
reconstruct the energy (enthalpy) profile of a reaction while QM-MM
VDWAALS energies are not included in DFTBESCF?
On Fri, Dec 17, 2010 at 1:18 AM, Andreas Goetz <agoetz.sdsc.edu> wrote:
> Dear Markus,
>
> The answer to all your questions below is 'yes'. You got everything right.
> Ross will send a more detailed email for anybody that didn't understand it so far.
>
> All the best,
> Andy
>
> For reference the links to earlier posts:
> http://archive.ambermd.org/201010/0503.html
> http://archive.ambermd.org/201011/0098.html
>
> On Dec 16, 2010, at 7:49 AM, Markus Kaukonen wrote:
>
>> Dear Amber,
>>
>> This issue has already been dealt with on this list, but I did not
>> quite get it, so here we go again:
>>
>> In QM/MM calculation with DFTB as QM engine one gets output like (with Amber10)
>>
>> NSTEP ENERGY RMS GMAX NAME NUMBER
>> 1 -2.1816E+04 1.7957E+01 1.4342E+02 C36 12502
>>
>> BOND = 2156.1278 ANGLE = 6029.2390 DIHED = 9228.7109
>> VDWAALS = -7560.4126 EEL = -52399.6187 EGB = -5475.9033
>> 1-4 VDW = 2123.9140 1-4 EEL = 37427.0797 RESTRAINT = 0.0000
>> DFTBESCF= -13345.6223
>>
>> Question: What is included in the term 'DFTBESCF'
>> Is it only the QM energy of the QM region (terminated with H atoms)
>> and electrostatic interaction of QM nuclei and electron cloud with
>> unscaled point charges of the MM region?
>>
>> Vdw interaction between QM and MM region is in included into 'VDWAALS'
>> and '1-4 VDW' ?
>> Possible bond, angle and dihedral terms between QM and MM regions are
>> included into the classical terms (BOND, ANGLE, DIHED)?
>> Solvation energy of QM region is in included into EGB ?
>>
>> Did I get it right?
>>
>> terveisin, Markus
>
> --
> Dr. Andreas W. Goetz
> San Diego Supercomputer Center
> Tel : +1-858-822-4771
> Email: agoetz.sdsc.edu
> Web : www.awgoetz.de
>
>
>
>
>
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>
--
Dmitry Nilov,
Lomonosov Moscow State University
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Received on Fri Dec 17 2010 - 05:00:04 PST
