Subject: Molecular modeling software for non-theorists?

From: [email-masked] (Julius Su)
Date: Mon, 9 Jun 1997 21:40:42 -0700 (PDT)

Hello,

  I work for a research group that uses laser spectroscopy to investigate
the basic dynamics of chemical systems on a short time scale.  Some 
members of our group have done fairly high level ab initio and molecular
dynamics simulations in the past; however, the main focus of the group
has definitely been experimental.  

  Because of this, there has been no standard way to model chemical
systems in our group.  Individuals in the group have either written
their own molecular dynamics routines or have had access to facilities
where programs like Gaussian 92 could be run, but no convenient in-group
facility to do simple molecular modeling has existed.          

  We are currently seeking to change this.  We would like to have some
standard way of finding the geometries of small to medium molecules
at a reasonable level of theory (semiemperical would be fine) and
for doing molecular dynamics of photoexcited systems.  This system
would have to be accessible and easy enough to use that any experimentalist
that wished to carry out an experiment would be able to quickly
throw together a rough simulation of the system in question.

  Our group plans to purchase two fairly high end PCs to run the
software that would be needed to do this.  I have recently purchased a
copy of Chem3D Pro with MOPAC for my personal use, and have found the
interface for molecule building and geometry optimization to be
intuitive and easy to use.  We also have some simple code that was
written within the group to do molecular dynamics on small clusters
of rigid molecules.  This code can be easily interfaced with Chem3D.

  Alternatively, we have found information on the Web about HyperChem,
which appears to have the ability to do model building, geometry optimization,
and a feature that would be especially useful to us, reactive molecular
dynamics.  It also appears to have facilities built in to visualize
vibrational modes and molecular oribtals (althought the latter feature
would not be nearly as important.)  Since our group already has a copy
of Gaussian 94, the added ab initio capabilities of the program are
nice but not essential.

  The main concern at this point, however, is how easy HyperChem would be 
to use.  Chem3D has impressed us with its intuitive interface and its
tight integration with ChemDraw.  We have not been able to find a 
demo of version of HyperChem with enabled building facilities to 
compare.  Since 90% of the time will probably be spent doing simple
model building and geometry optimization, this is particularly      
important to us.

  So, has anyone on this list had experience with HyperChem and Chem3D?
How easy is it to build molecules in HyperChem?  Does it have a 
reasonably useable interface?  Can it generate publication quality
graphics?  Can experimentalists who don't want to spend too much
time learning the nitty-gritty of semiemperical theory do simple
calculations using it?

  Thank you very much for your help.

Later,

Julius Su
[email-masked]