[gmx-users] Tabulated potentials

[Alessandra Villa]

Hi,

On Wed, Feb 12, 2020 at 10:59 PM Ali Khodayari <
ali.khodayari at student.kuleuven.be> wrote:

> 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:
>
>
In topol.top one specifies which table is used for which interaction (bond,
angle, dihedral). See the table below for the synthases

http://manual.gromacs.org/documentation/current/reference-manual/topologies/topology-file-formats.html#topology-file

Best regards
Alessandra



> 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
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