[gmx-users] Gromacs tabulated potentials for CG models

[Sudip Das]

Dear All,

I want to use Gromacs to simulate my coarse-grain model. Our group
developed the coarse-grain parameters for the system of interest. The
non-bonded parameters are having a different potential form for different
pairs. I came across a documentation (
http://www.gromacs.org/@api/deki/files/94/=gromacs_nb.pdf)
where we can use a different potential form in a simulation. Here I am
attaching the itp file.

While I am running the NVT equilibration on the system using 4 cores, the
simulation is running fine, but when I am using the same configuration on
more than 4 cores, I am getting an error saying that,

Fatal error:
1 of the 35535 bonded interactions could not be calculated because some
atoms involved moved further apart than the multi-body cut-off distance
(1.4 nm) or the two-body cut-off distance (1.4 nm), see option -rdd, for
pairs and tabulated bonds also see option -ddcheck

I want to know how to rectify this problem.

Eagerly, waiting for your reply.

Thanks in advanced.

Regards,
Sudip Das

PhD Student
C/o. Prof. S. Balasubramanian
Molecular Simulations Lab
Chemistry and Physics of Materials Unit (CPMU)
Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR)
Bangalore, India
‌