From: Christopher Harrison (char_at_ks.uiuc.edu)
Date: Thu Aug 30 2007 - 08:30:05 CDT
Hi Dow,
The scalability of NAMD remains one of it's greatest strengths.
While the QM calculation will be the bottleneck for speed in most
QMMM calculations, we hope to maintain the scalability of NAMD's MD
within QMMM.
Whatever the outcome, to be very clear about this: the scalability
and speed of NAMD MD, which many users depend upon, will in NOT be
negatively altered. :-)
Best,
Chris
On Aug 30, 2007, at 12:02 AM, Dow_Hurst wrote:
> 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
>>
>
> No sig.
>
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:45:11 CST