[gmx-users] new MD package

[CORINA BARBU]

Hello!

Does anybody know about a package capable of doing molecular dynamics
simulations with semiempirical methods(i.e. tight-binding, for example PM3) and
which runs in parallel? Something like GROMACS but using instead of a molecular
mechanics potential a tight-binding method. I know about HyperChem but this
runs on a PC and it is not open source and I approximated that it would take me
about 200h for a single simulation... 

Thanks! Corina


PS: For people who suggested me to use Prodrg to generate a top file and take
initial charges: it doen't seem to have all of the atoms that I need in my
molecule.






On Fri, 24 Oct 2003 23:37:31 +0200, David wrote:

> On Fri, 2003-10-24 at 01:27, Ilya Chorny wrote:
> > How does one compile just the tools like g_sas or g_sorient?
> > 
> you stil have to compile gmxlib and mdlib, so might as well install the
> whole thing (but in another directory!)
> 
> > Ilya
> > 
> > On Wed, 2003-10-22 at 12:53, Ilya Chorny wrote:
> > > Hello,
> > > 
> > > I am trying to use g_sorient to calculate the solvent orientation around
> > > my solute. To test g_sorient I created a gro file the has one Atom and
> > > one H2O molecule in  the following orientation.
> > > 
> > >          H
> > > A --- O
> > >          H
> > > 
> > > When I look at the output files for I see a distribution for theta 1
> > > peaked at 90 degrees and a distribution for theta 2 peaked at 90
> > > degrees. Three question: 1.) Why do I see a distribution? I would expect
> > > only one point. 2.) Why is theta 1 peaked at 90 degrees? Based on the
> > > definition in the manual it should be either 0 or Pi. 3.) Does g_sorient
> > > normalize the angles.
> > > 
> > > Thanks
> > > 
> > > 
> > > Ilya
> > 
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> -- 
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Assist. 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://xray.bmc.uu.se/~spoel
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