Error in minimization gromacs

User discussions
1

GROMACS version:
GROMACS modification: Yes/No
Here post your question
sorry here is the drop box link to look into gromacs input generated using CharmmGUI.

Dropbox

gromacs.zip

Shared with Dropbox

The minimization is stuck at md run minimization steps and returns following error.
error at the minimization step:

  • first, a warning from the software at the beginning :
    "WARNING: Listed nonbonded interaction between particles 31319 and 31334
    at distance 2.863 which is larger than the table limit 2.260 nm.

This is likely either a 1,4 interaction, or a listed interaction inside
a smaller molecule you are decoupling during a free energy calculation.
Since interactions at distances beyond the table cannot be computed,
they are skipped until they are inside the table limit again. You will
only see this message once, even if it occurs for several interactions."

  • then the program crashes after 17 steps of minimization:
    “step 17: One or more water molecules can not be settled.
    Check for bad contacts and/or reduce the timestep if appropriate.
    16736 16735 40.5 0.0997 0.0997 0.0997”

and system/run is hanged beyond this.

IMPORTANT: This should not happen in a stable simulation, so there is
probably something wrong with your system. Only change the table-extension
distance in the mdp file if you are really sure that is the reason."

Please advice

many thanks in advance,
Urvashi Sharma

2

I used gromacs-2020.1 with double precision to reproduce the error, but I couldn’t. Try switch to double precision if you used single precision.

3

Hello

I too face the same error, like EM stopping with a similar messages.
I am using 2018.8 gromacs and would like to know how to incorporate double precision
Thank you…

4

add -DGMX_DOUBLE=on during CMake configuration.

5

Can we do this after gromacs has already been installed?
[-DGMX_DOUBLE=on]

6

No, You can’t. Precision are set during compile time.