Hello Carsten, Thanks for your reply! The system I'm testing is a 128x128x128 nm box containing only water. I tried using double precision, but the error is the same. There are lots of errors like this:
Program: gmx mdrun, version 2019.3 Source file: src/gromacs/mdlib/nbnxn_grid.cpp (line 1164) MPI rank: 9 (out of 16) Fatal error: grid cell cx -207 cy 0 out of range (max 23 372) atom 0.000000 0.000000 0.000000, grid->c0 72.000000 0.000000 There are many atoms with coordinates 0.000000 0.000000 0.000000, which I think should be an error. Zhang > -----原始邮件----- > 发件人: "Kutzner, Carsten" <ckut...@gwdg.de> > 发送时间: 2019-07-09 22:03:06 (星期二) > 收件人: "<gmx-us...@gromacs.org> GROMACS users" <gmx-us...@gromacs.org> > 抄送: > 主题: Re: [gmx-users] what's the maximum number of atoms that GROMACS can > simulate? > > Hi Zhang, > > > On 9. Jul 2019, at 15:16, 张驭洲 <zhangyuzho...@mails.ucas.edu.cn> wrote: > > > > Hello， > > > > I want to know if there is a maximum number of atoms that GROMACS can > > simulate, or if there are any bugs in the code that cause the error in > > computing the coordinate of atoms when the number of atoms is very large? > > I'm trying to simulate some very large systems using GROMACS-2019.3. > > Unfortunately, the energy minimization crashed during the run. I tried > > using more than one compute nodes, for example, 4, 8 or 32, and I'm sure > > the memory is not exhausted. The system I tried contains more than 100 > > million atoms. > There is no limit on the number of atoms that you can simulate in GROMACS. > > However, if the simulation systems become very large in at least one > dimension, > you might need double precision, as single precision could be insufficient > to accurately store the positions of atoms that are far off the origin. > This can then lead to a positive energy drift which could become so large > that the system gets instable. > > A while time ago we have observed such problems with large systems of mostly > vacuum, which contained several water droplets. The droplets that were > farthest > away from the origin would start to heat up and eventually evaporate after > some time, unless a double precision version of mdrun was used. > > Carsten > > > > > > Zhang > > -- > > 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 gmx-users-requ...@gromacs.org. > > -- > Dr. Carsten Kutzner > Max Planck Institute for Biophysical Chemistry > Theoretical and Computational Biophysics > Am Fassberg 11, 37077 Goettingen, Germany > Tel. +49-551-2012313, Fax: +49-551-2012302 > http://www.mpibpc.mpg.de/grubmueller/kutzner > http://www.mpibpc.mpg.de/grubmueller/sppexa > > -- > 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 gmx-users-requ...@gromacs.org. -- 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 gmx-users-requ...@gromacs.org.
