[gmx-users] atom types @ bonded parameters

[Francesco Pietra]

Thanks.
The molecules have no repetitive units, though they
have recurring moieties, such as five-membered to
nine-membered saturated heterocycles, variously
substituted. Is it safe to carry out the frequency
task on each type of recurring moiety? I understand
that without seeing it is difficult to judge, though
my concept should be clear: evaluating the bonded
parameters from sections of the actual molecule.

With my molecules of 90 to 450 atoms, a QM geometry
optimization/frequence calculation would be too time
consuming at DFT theory, if a reliable functional and
basis set is choose.

Thanks
francesco 



--- David van der Spoel <spoel at xray.bmc.uu.se> wrote:

> Francesco Pietra wrote:
> > New to the list, aimed at installing gromacs on
> Linux
> > Debian amd64 dual-core-opterons for parallel
> > execution, I would appreciate indications where
> (not
> > having yet installed gromacs) to find: 
> > 
> > ---Atom types list.
> > ---Bonded parameters list.
> > ---Any tool to generate new bonded parameters.
> > 
> share/gromacs/top
> 
> > I am well equipped of QM suites and have also some
> > experience with classical MD. My problem was
> always
> > lack of bonded parameters and atom types that I
> need
> > for my studies.
> 
> If you kow your QM a frequency calculation of your
> molecule should give 
> you force constants and optimization the equilibrium
> distances and 
> angles. only problem is torsion parameters. for
> these you have to read 
> the appropriate force field papers.
> 
> > 
> > Thanks
> > 
> > francesco pietra
> > (This is a project of mine of long date, and I
> also
> > had exchange of emails with the Debian gromacs
> > maintainer; though, it is only now that I have the
> > time to try to start).
> > 
> > 
> >        
> >
>
____________________________________________________________________________________Pinpoint
> customers who are looking for what you sell. 
> > http://searchmarketing.yahoo.com/
> > _______________________________________________
> > gmx-users mailing list    gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at
> http://www.gromacs.org/search before posting!
> > Please don't post (un)subscribe requests to the
> list. Use the 
> > www interface or send it to
> gmx-users-request at gromacs.org.
> > Can't post? Read
> http://www.gromacs.org/mailing_lists/users.php
> 
> 
> -- 
> David.
>
________________________________________________________________________
> David van der Spoel, PhD, Assoc. Prof., Molecular
> Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala
> University.
> Husargatan 3, Box 596,  	75124 Uppsala, Sweden
> phone:	46 18 471 4205		fax: 46 18 511 755
> spoel at xray.bmc.uu.se	spoel at gromacs.org  
> http://folding.bmc.uu.se
>
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the
> list. Use the 
> www interface or send it to
> gmx-users-request at gromacs.org.
> Can't post? Read
> http://www.gromacs.org/mailing_lists/users.php
> 



       
____________________________________________________________________________________Take the Internet to Go: Yahoo!Go puts the Internet in your pocket: mail, news, photos & more. 
http://mobile.yahoo.com/go?refer=1GNXIC