[gmx-users] Three-site model for acetonitrile
David van der Spoel
spoel at xray.bmc.uu.se
Mon Feb 24 19:43:44 CET 2003
On Mon, 2003-02-24 at 15:01, Christoph Freudenberger wrote:
> David van der Spoel wrote:
> > How about energy? Any idea if the potential energy is OK for your
> > system?
> I just compared the the potential energy of the MeCN-System with that
> of my other systems:
> MeCN: -3500 KJ/mol (or whatever comes out of g_energy)
> CH2Cl2: -6000
> MeOH: -13800
> DMSO: -21300
> The Systems do contain different numbers of atoms, I don't know if that
> makes any diffrence for the values calculated by g_energy.
Of course, you have to divide by the number of molecules -nmol option
for g_energy, or do it afterwards.
You also want to check the density in a constant pressure simulation.
> > How do you keep it linear? You probably want to define a
> > topology with a dummy for this..
> I do not use any constraints. While double-checking the forcefield
> of MeCN i realized, I had set the bond length of the C-N triple bond
> to small (0.1nm instead of 0.116nm).
This will make a difference...
Dr. David van der Spoel, Dept. of Cell & Mol. 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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