Fatal error: Free Energy Analysis

User discussions
1

GROMACS version: 2018.8
GROMACS modification: Yes

Hello,

I am currently running a free-energy analysis on my DNA structure at different solvent. During the NVT run at dhdl value of 0, an error occur:
######################
Fatal error:
2 of the 352793 bonded interactions could not be calculated because some atoms
involved moved further apart than the multi-body cut-off distance (5.0796 nm)
or the two-body cut-off distance (5.0796 nm), see option -rdd, for pairs and
tabulated bonds also see option -ddcheck
######################

Note that I didn’t use -rdd or -dds option. My command is shown below:

gmx mdrun -v -ntmpi 4 -ntomp 16 -gpu_id 0 -ddcheck -deffnm nvt$LAMBDA

Can someone help me on this problem? Thank you very much and have a great day!

2

Hi,

-rdd is set automatically for you, if this setup usually works and only fails in this specific case, you can try increasing the default value by explicitely setting -rdd to a higher value or using fewer cores, resepctively domains for your simulation.

Best,
Christian

3

Hello,

If increasing the -rdd value is not possible, do I need to decrease the number of cores in order to run the NVT emsemble?

Thank you.

Sincerely,
Alexis

4

Yes, that might solve the issue.

5

Thank you very much.