[gmx-users] what's the maximum number of atoms that GROMACS can simulate?

[张驭洲]

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" <ckutzne at gwdg.de>
> 发送时间: 2019-07-09 22:03:06 (星期二)
> 收件人: "<gmx-users at gromacs.org> GROMACS users" <gmx-users at 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 <zhangyuzhou15 at 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
> > -- 
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> --
> 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
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