[gmx-users] SiO2 simulation again.

David van der Spoel spoel at xray.bmc.uu.se
Sat May 4 11:45:20 CEST 2002

On Fri, 3 May 2002, Lianqing Zheng wrote:

>Hi, David:
>I did get that error when I didn't use directives [moleculetype] nor
>[atoms]. But with current .top file, I could get a .tpr.
>What do you mean by "sort"? Where should I sort atoms in top file? At
>[molecules]? And in gro file, should I make it such that the first 1024
>atoms are O and rest of them SI?
This is correct. In the top file you specify
Si N
O  M

the gro file should have the same order.

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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