[gmx-users] Tabulated potentials

[Ali Khodayari]

Dear Gromacs users,

I’ve got a question regarding the tabulated potentials for bonded interactions.

Gromacs recognises and reads the non-bonded potential tables through the energy groups specified. But how can I refer each bond type to its table?

I have derived coarse-grained potentials for a cellobiose-water system. There are 11 beads (4 bead types) in each cellobiose molecule, and each water molecule is coarse-grained as one bead. Overall, there are 3 bonded terms for 3 bond types, 3 anglular potentials for 3 angle types, and 2 dihedral potential tables for two types of dihedrals. The tables are named as table_b1.xvg, table_b2.xvg, and so on.

Now my question is, how does gromacs recognise which table is regarding which bonded term? The simulation crashes at the very beginning giving me the following error:

A tabulated bond interaction table number 1 is out of the table range: r
0.511823, between table indices 511 and 512, table length 501

I believe this is caused due to high forces on atoms indeed, but it might be also because tables are not specified to the correct bond type.


Kind regards,
Ali