[gmx-users] SiO2 simulation again.

David van der Spoel spoel at xray.bmc.uu.se
Fri May 3 23:08:23 CEST 2002

On Fri, 3 May 2002, Lianqing Zheng wrote:

>I am trying to simulate an all-atom (no bonded interaction) system of SiO2
>with Coulomb and Buckingham potentials. The following are the .top and
>.gro files that I constructed. Do you know if there is any error or flaw
>in them? When I ran mdrun, I got an error of "Arithmetic Exception (core
>dumped)." Though it could be many reasons, I don't know if I made the
>format of top and gro files right with the system. Could you take a
>minute to check them?
You probably got an error message from grompp saying:
atomnames in topology do not match coordinate file.

You should sort the atoms in the coordinate file the same was as in the
topology file. 

Groeten, David.
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel

More information about the gromacs.org_gmx-users mailing list