[gmx-users] A question about simulation system includes more than 100000 atoms using Gromacs

[Jan Jirsák]

Hi Zhuquing,

as far as I know, atom numbers in .gro file are irrelevant - gromacs
asigns indices based on the order of records in the file. I my
configurations numbers are often quite random, as I copy and paste
coordinates from different sources. It never caused any problems in
gromacs (neverheless, it can cause troubles in visualisation
software).

Regards,
Jan

2015-07-19 12:10 GMT+02:00 张竹青 <zhuqingzhang at ucas.ac.cn>:
> Dear Madam/Sir,
>
>   I have recently tried to use Gromacs to simulation a biolmoleculal system including more than 100000 atoms. As usually, the .gro file just supports the system with atom number up to 99999. But there are some publications in which researchers used Gromacs to simulate like ribosom systems, which includes more than 2000000 atoms. So, could you give some advice on how to do it? Does it need to change the source codes?
>
>   Thanks,
>
>   Zhuqing
>
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