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

[张竹青]

Hi Jan,

  Thank you very much for your reply.

  I tried to use pdb2gmx (gromacs v4.5.5), in fact, for the chain with the atom number serial larger than 10000 in pdb file, it can bot be recognized.

  Best,

  Zhuqing


> -----原始邮件-----
> 发件人: "Jan Jirsák" <janjirsak at gmail.com>
> 发送时间: 2015年7月19日 星期日
> 收件人: gmx-users at gromacs.org
> 抄送: 
> 主题: Re: [gmx-users] A question about simulation system includes more than 100000 atoms using Gromacs
> 
> 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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