Dear Gromacs users,
We have an old coarse-grained polymer model with graphene (~ 3100 coarse-grained beads) that was built using the Inverse Boltzmann Iterative procedure with the help of VOTCA. This model is simulated without errors and warnings when gromacs 4.6.5 is employed with particle decomposition flag (-pd). We compared the results of CG simulation with the atomistic model, and there is no difference in structural properties, and as for all CG models the dynamics is faster than in the atomistic model. However, when we switched the simulation to Gromacs version 5.1.4 in which it does not implement particle decomposition, the simulation did not start and the following error appears.
Fatal error:
28 of the 7134 bonded interactions could not be calculated because some atoms involved moved further apart than the multi-body cut-off distance (2 nm) or the two-body cut-off distance (2 nm), see option -rdd, for pairs and tabulated bonds also see option -ddcheck
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
Is it simple way to switch from particle decomposition to domain decomposition to use new versions of Gromacs?