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" <[email protected]> > 发送时间: 2015年7月19日 星期日 > 收件人: [email protected] > 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 <[email protected]>: > > 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 > > > > > > > > > > > > > > > > > > > > > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send > > a mail to [email protected]. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to [email protected]. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to [email protected].
