[ghemical-devel] Re: Ghemical

[Francesco Pietra]

hi geoff
thank you for taking care of my problems. hope the discussion can help others 
too. see below 

On Monday 03 April 2006 16:50, Geoffrey Hutchison wrote:
> Ciao Francesco,
>
> I'm forwarding your message to the Ghemical mailing list and will
> make a few comments. I certainly appreciate your feedback -- it's
> good to hear from users. (By the way, what do you describe as "large"
> molecules? 40-50 atoms? More?)
current problems with natural products made of 44 carbons plus 5 oxygens, 2 
nitrogens and hydrogens to fulfill valency.
>
> I agree with the difficulty in running DFT jobs under MPQC in
> Ghemical right now. One workaround, obviously is to use the "export"
> feature to write an MPQC input file directly. This has the advantage
> of running a batch of MPQC jobs on another computer (which is what I
> usually do with GAMESS or MPQC).
yes, this is just what i do with mpqc, using internal or cartesian coordinates 
from the MM minimizer output to input ab initio.
>
> You mention "lack of a modern molecular mechanics program" for
> "reasonably minimized conformers." I'm not sure what you mean -- I've
> done Monte Carlo conformer searching using Ghemical and found pretty
> reasonable conformers. In fact, I think the MC searching algorithm in
> Ghemical is pretty good -- often finding better candidates than other
> programs. While Ghemical doesn't offer tons of MM force fields, I
> think its MM parameters are pretty decent.
i never used montecarlo before because i tought it is for biopolymers like 
proteins; my molecules are of the organic type: no repeating units, multiple 
rings, bridgeheads, and, keypoint, unsaturated bonds. in fact, i had a brief 
trial with my molecules by montecarlo on ghemical but i was unable to get a 
map of local minima (i had established by other MM ways a large number of 
minima witin a 1.5 kcal/mol window)
>
> I'm not sure when the Ghemical-2.0 release will happen, but I suspect
> that Michael Banck will try to get a Debian package fairly soon --
> he's one of the developers of Ghemical too.
i look forward to installing the new version of ghemical.

finally, i hope that my criticism was not taken by anyone as adverse 
criticism; when i use the word "criticism" i always mean "constructive 
criticism"; the problem is if it may be really constructive....

best wishes
francesco
>
> Best regards,
> -Geoff
>
> > version installed on my debian testing/unstable is 1.91-2.
> >
> > making clear that i am a natural product chemist, therefore
> > interested in
> > computation for "large" organic molecules, the problems i noticed,
> > and which
> > let me set aside ghemical for the time being, are:
> >
> > --lack of input to mqcp for DFT calculations (many body
> > calculations cannot be
> > carried out on my molecules; choosing a restrited basis set, they are
> > useless);
> >
> > --lack of a modern  molecular mechanics program to input to mqcp
> > reasonably
> > minimized conformers.
> >
> > although i am quite new to mqcp i am investing on it (to escape
> > institutional
> > restrctions for cpu time, i am building at home a workstation based
> > on a
> > couple of dual core amd64 opterons on a tyan k8we mainboard and a
> > couple of
> > hd raid1 300GB each and i plan to feed it debian testing). i was
> > attracted by
> > the native conception of mqcp for parallel calculations, so that i
> > am even
> > planning to change to it on mainframe. i have experimented a few
> > calculations
> > on a amd athlon 1ghz and found them absolutely faster than on
> > gamess (i do
> > not know gaussian which is used by my colleagues: i believe that
> > carrying out
> > molecular calculations blindly on proprietary software is a waste
> > of time)
> >
> > that said, it will take time before i am ready to carry out
> > calculations on
> > the new workstation. however, i am extremely interested in the new
> > version of
> > ghemical. certainly an input to ab initio from a graphical
> > interface relieves
> > fro the hardest problems if the molecule is large. it would be
> > great if you
> > can provide me a debian package in advance (please the package
> > because these
> > trials are during spare time: the burden of normal duties is heavy
> > indeed and
> > compilations normally take time).
> >
> > finally, thank you very much for contacting me. it was great pleasure
> >
> > francesco
> >
> > On Friday 31 March 2006 02:28, you wrote:
> >> Dear Francesco,
> >>
> >> While there are other open QM programs, I can certainly understand
> >> your choice of MPQC. Have you checked out the free program Ghemical?
> >> The current development version for v2.0 is quite good -- I use it
> >> for molecular mechanics and conformational analysis daily. I'd be
> >> glad to send you a "snapshot," or you can wait a few weeks for v2.0
> >> to be released.
> >>
> >> http://www.uku.fi/~thassine/ghemical/
> >>
> >> (Incidentally, Ghemical uses Open Babel for file import/export,
> >> although pieces exist to run MPQC and MOPAC directly, and support for
> >> GAMESS-US has been contributed recently.)
> >>
> >> Cheers,
> >> -Geoff
> >>
> >> On Mar 29, 2006, at 2:36 PM, Francesco Pietra wrote:
> >>> preoccupied because i am investing in mpqc for my computational
> >>> future,
> >>> abandoning other software.
> >>>
> >>> the generation of unambiguous coordinates for all atoms of a
> >>> complex organic
> >>> molecules (from 20 to 40 carbons, plus all other atoms, IDROGENS
> >>> INCLUDED) is
> >>> what i need to build an input for ab initio computation. and the
> >>> generation
> >>> can only be from graphics, because it is only the graphics that
> >>> allows
> >>> debugging in case of complex molecules (unless one aims at doing
> >>> that by
> >>> inspection of dreiding model and with the aid of mechanicall metric
> >>> tools,
> >>> which, however, will never work). and the input to mpqc must be
> >>> from well
> >>> minimized conformers through a modern force field, otherwise there
> >>> is no hope
> >>> for any ab initio method.
> >>>
> >>> which talk is not to disregard the work that is being done around.
> >>> difficult,
> >>> heavy work. but the competion of proprietary software is severe.
> >>> most of this
> >>> creates only illusion, but the atomic coordinates are generated
> >>> accurately.