[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...

Groeten, David.
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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