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.
