[gmx-users] Issues with huge system

Kevin Chen fch6699 at gmail.com
Fri Nov 4 22:09:32 CET 2016

Hi Gromacs Users,


We 've observed  some issues while creating huge simulation boxes (over35
nm* 35 nm * 35nm in size). Commands used for building our benchmarks showed
as follow:

gmx pdb2gmx -f 1AKI.pdb -o 1AKI_processed.gro -water spce

gmx editconf -f 1AKI_processed.gro -o 1AKI_newbox.gro -c -box 33 33 33 -bt

gmx solvate -cp 1AKI_newbox.gro -cs spc216.gro -o 1AKI_solv.gro -p topol.top

gmx grompp -f ions.mdp -c 1AKI_solv.gro -p topol.top -o ions.tpr

gmx genion -s ions.tpr -o 1AKI_solv_ions.gro -p topol.top -pname NA -nname
CL -nn 8

gmx grompp -f minim.mdp -c 1AKI_solv_ions.gro -p topol.top -o em.tpr

The problem only showed up when using box size greater than 30nm * 30nm * 30
nm. Once the box is bigger than 30*30*30, the simulation always crashes
during EM stage. However everything is fine when using any box sizes smaller
than 30*30*30.   As such, we are eager to know if that was something we did
wrong or there's some sort of issues for Gromacs dealing with large systems.
Any suggestions and pointers are welcome!

Thanks in advance,


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