[gmx-users] 3dc + GPU

Mark Abraham mark.j.abraham at gmail.com
Wed Jul 9 20:49:09 CEST 2014

On Jul 9, 2014 7:39 PM, "Ondrej Kroutil" <okroutil at gmail.com> wrote:
> Hi gromacs users and developers,
> I have troubles with simulations of the system with surface (slab
> using GPU and Verlet cut-off scheme.
> When I run this simulation on CPU everything goes right and ions dissolved
> in the water above the surface seems to behave normally. But when I switch
> to GPU positively charged ions move in z-direction to the bottom of the
> simulation box and negatively charged ions go to opposite side of the box.
> I have had this problem with 4.6 version and now even with version 5.0.
> Do you have any suggestion what can be wrong? Bad input parameters? Etc.
> You can download tar file with input file, .tpr file (if you want to run
> on your system, output log and pictures of initial and final state)
> Thank you very much and keep developing Gromacs, the best simulation
> package ever!
> Ondřej
> Btw.: How can I set-up in gromacs-5.0 to run simulations only on CPU?

No idea for the main issue, but cmake -DGMX_GPU=off or running as mdrun -nb
CPU are different ways to do what you want.


> --
> Ondřej Kroutil
>         ,,              Faculty of Health and Social Studies
>    ----"))'             University of South Bohemia
>      OOO           Jirovcova 24, Ceske Budejovice
>       OOO          The Czech Republic
>         | OO         E-mail:  okroutil at gmail.com
> >------    O         Mobile:  +420 736 537 190
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