Re: About QM-MM

From: Francesco Pietra (chiendarret_at_yahoo.com)
Date: Wed Aug 29 2007 - 11:54:12 CDT

Hi Dhiraj:
You are right, NWChem is not open source. Though, free license - including
source code - is given for no-profit work.
francesco

--- Dhiraj Srivastava <dhirajks_at_gmail.com> wrote:

> Hi
> from GAMESS-US you can do semiempirical, DFT and other higher level
> calculation. so you can do any level of calculation you want with
> GAMESS-US. I was thinking NWChem is not open source.
> Dhiraj
>
>
> On 8/29/07, Francesco Pietra <chiendarret_at_yahoo.com> wrote:
> >
> > I don't know Gamess-US (I use NWChem). Are you talking of semiempirical or
> > "ab
> > initio" QM? Of course, "ab initio" wouldn't be viable for molecules from
> > medium
> > size (60 atoms) on.
> > francesco
> >
> > --- Dhiraj Srivastava <dhirajks_at_gmail.com> wrote:
> >
> > > Hi
> > > If you can interface NAMD with some open source QM package like
> > GAMESS-US
> > > then it will be good. then both NAMD and QM package will be open source.
> > > Dhiraj
> > >
> > > On 8/29/07, Francesco Pietra <chiendarret_at_yahoo.com> wrote:
> > > >
> > > > The problem is not open or closed source (you can have ONION in open
> > > > source QM
> > > > suites, as I have it). ONION is quite a different affairs from QM-MM.
> > > >
> > > > francesco
> > > >
> > > > --- Eduardo Tejera <edutp00_at_yahoo.com> wrote:
> > > >
> > > > > These are great news without any questions.
> > > > >
> > > > > I think that is very intersting the problem of interaction between
> > > > small
> > > > > molecules and proteins were the QM-MM can be applied as a very
> > usefull
> > > > tool.
> > > > > We can use ONION in Gaussian with good results in several case but
> > this
> > > > > software is not open source like NAMD and with the posibility of
> > > > "scripts"
> > > > > the spectrum of applications is very wide. I think that the use of
> > > > > semiempirical methods as well as DFT could be available.
> > > > >
> > > > > Best
> > > > > Eduardo
> > > > >
> > > > > Francesco Pietra <chiendarret_at_yahoo.com> escribió:
> > > > > Hi Chris:
> > > > > These are wonderful news.
> > > > >
> > > > > Of my interest is the interaction of the "organic molecule" (read:
> > > > natural
> > > > > products, drugs) with biopolymers. Even the first simple step of
> > > > studying the
> > > > >
> > > > > conformations of the "organic molecule" under the influence of the
> > > > > environment
> > > > > could be best approached by QM-MM.
> > > > >
> > > > > I foresee two problems:
> > > > > (1) Semiempiricals like MNDO, PM3, AM1 deal very poorly with
> > > > conformational
> > > > > problems. Perhaps, DFTB is better to this respect.
> > > > > (2) Parameters for the "organic molecules". However, Jan Saam just a
> > few
> > > > days
> > > > > ago has promised to develop Paratool, once is PhD examinations are
> > over.
> > > > > Paratool could solve these problems, provided it is made simple
> > > > (automatic)
> > > > > enough to become manageable by the organic chemist.
> > > > >
> > > > > Best wishes
> > > > >
> > > > > francesco pietra
> > > > >
> > > > > --- Christopher Harrison wrote:
> > > > >
> > > > > > 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
> > > > > > >
> > > > > >
> > > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > >
> > > >
> > >
> >
> >
>
____________________________________________________________________________________
> > > > > Building a website is a piece of cake. Yahoo! Small Business gives
> > you
> > > > all
> > > > > the tools to get online.
> > > > > http://smallbusiness.yahoo.com/webhosting
> > > > >
> > > > >
> > > > >
> > > > > __________________________________________________
> > > > > Correo Yahoo!
> > > > > Espacio para todos tus mensajes, antivirus y antispam ¡gratis!
> > > > > Regístrate ya - http://correo.espanol.yahoo.com/
> > > >
> > > >
> > > >
> > > >
> > > >
> > >
> >
> >
>
____________________________________________________________________________________
> > > > Shape Yahoo! in your own image. Join our Network Research Panel
> > today!
> > > > http://surveylink.yahoo.com/gmrs/yahoo_panel_invite.asp?a=7
> > > >
> > > >
> > > >
> > >
> > >
> > > --
> > > Dhiraj K. Srivastava
> > > Department of Chemistry
> > > University of Missouri-Columbia
> > > MO, 65211
> > > Ph. no. 001-573-639-0153
> > >
> >
> >
> >
> >
> >
>
____________________________________________________________________________________
> > Shape Yahoo! in your own image. Join our Network Research Panel today!
> > http://surveylink.yahoo.com/gmrs/yahoo_panel_invite.asp?a=7
> >
> >
> >
>
>
> --
> Dhiraj K. Srivastava
> Department of Chemistry
> University of Missouri-Columbia
> MO, 65211
> Ph. no. 001-573-639-0153
>

      ____________________________________________________________________________________
Luggage? GPS? Comic books?
Check out fitting gifts for grads at Yahoo! Search
http://search.yahoo.com/search?fr=oni_on_mail&p=graduation+gifts&cs=bz

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 05:20:33 CST