GROMACS version: 2020.2
GROMACS modification: No
While doing some AWH scans of the ligand complexes with proteins and DNA, I sometimes get the errors at some unpredictable points in the simulation
Distance between pull groups 3 and 10 (5.204208 nm) is larger than 0.49 times the box size (5.203962).
In previous cases I was able to work around it by including an additional restraining potential that supposedly prevented the ligand from going too far. However, with the recent system (DNA 28-mer + organic ligand in water box) I was not so lucky.
Moreover, I cannot understand why the error occurs when it does. I also wonder what the correct options should be and/or if the logic in pull code might actually be incorrect.
So, the box is actually quite large (10.6 nm including 1 nm margin on all sides) and the flat-bottom restraint is set at 5 nm. However, the system never reaches that distance. In the last run, it started at 1.9 nm and crashed soon after 3.35 nm. I guess that, due to some random drift of molecules, the pull code suddenly finds another periodic image of one or both molecules more “attractive”, leading to this discontinuity.
I tried playing with
pull-groupN-pbcatom, and COM motion removal options (even tried setting the ligand
pbcatom to another molecule’s reference) but to no avail. Increasing the box size obviously would not help either, as the desired distance is not reached anyway (but the simulation would take longer to crash)))).