[gmx-users] torsion potential again
spoel at xray.bmc.uu.se
Fri May 16 22:22:00 CEST 2003
On Fri, 2003-05-16 at 20:35, B. Nick wrote:
> > On Thu, 2003-05-15 at 22:01, B. Nick wrote:
> > > Dear all,
> > >
> > > is there a simple way (using the implemented
> > > tools) to systematically vary specific dihedrals
> > > of molecules to plot the torsion potential vs
> > > torsion angle?
> > No.
> > Complicated way would be using an external tool like molden and write
> > out pdb files. If you only want to see the torsion potential you can use
> > a spreadsheet, or xmgrace, but I assume you want to see the total energy
> > (and compare to quantum calculations?)
> This is exactly what I want to do, but is it
> really possible to rotate dihedrals with molden
> and write multiple pdb-files?
> I downloaded and installed molden successfully,
> but was not able to rotate a single dihedral
> systematically with this program.
Yes, you go into the Z-matrix editor, edit the dihedral of your choosing
to an exact angle and then close the Z-matrix editor again and write the
pdb file. It is a bit tedious though. Actually, other tools like pymol
may do these things in a simpler way.
Dr. David van der Spoel, Dept. of Cell and Molecular Biology
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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