Re: About QM-MM

From: Francesco Pietra (chiendarret_at_yahoo.com)
Date: Thu Aug 30 2007 - 00:50:35 CDT

I am no developer,though QM-MM would certainly affect the scalability.
Diagonalization of matrices that come at no peace poses harsh problems -
perhaps never solved so far - to parallelization. However, QM-MM, if not
activated, could not affect any other procedures by NAMD, I guess. The word to
developers.

francesco

--- Dow_Hurst <dhurst_at_mindspring.com> wrote:

---------------------------------
body{font-family:
Geneva,Arial,Helvetica,sans-serif;font-size:9pt;background-color:
#ffffff;color: black;}Our group would certainly be interested in QM/MM
implemented in NAMD. However, we would not want the scalability of NAMD to be
affected adversely when using the QM/MM functionality. It would be great to
approach the QM part of the calculation from that perspective.
Thanks,
Dow

-----Original Message-----
From: Christopher Harrison
Sent: Aug 28, 2007 1:42 PM
To: Francesco Pietra
Cc: namd-l_at_ks.uiuc.edu
Subject: Re: namd-l: About QM-MM

Hi Francesco,

We are currently in the early stages of planning and developing a QM-MM
implementation for NAMD. There's obvious interest from the community as well
as our own group for this functionality.

We'd be happy to hear about any specific types of QM-MM calculations,
functionalities or applications that might be useful to those interested.

Best,
Chris

 Christopher Harrison
Postdoctoral Research Associate
Theoretical and Computational Biophysics Group
University of Illinois at Urbana-Champaign
char_at_ks.uiuc.edu

 

On Aug 28, 2007, at 8:18 AM, Francesco Pietra wrote:

I wonder why no QM-MM in NAMD. Is that because of disbelief in semiempirical
electronic calculations, such as MNDO AM1 PM3 DFTB, or is just because no
developer has yet had time to consider that facet?

The other side of the coin is MD included in well established QM code suites,
which become unmanageable with molecules of common interest.

These are not intended to be provocative questions. To the contrary, views
about QM-MM from the two sides may help planning research in the scientific
community.

Thanks

francesco pietra

 

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