[gmx-users] SiO2 simulation again.

[David van der Spoel]

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
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