[gmx-users] Tabulated potentials

[Ali Khodayari]

Thank you Alessandra. However, fixing the topology did not remove the error. It still stands as before:

A tabulated bond interaction table number 4 is out of the table range: r
0.575410, between table indices 575 and 576, table length 501

Anyone has any idea why it could be happening?

My best,
Ali



-----Original Message-----
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> On Behalf Of Alessandra Villa
Sent: donderdag 13 februari 2020 16:28
To: gmx-users at gromacs.org; gromacs.org_gmx-users <gromacs.org_gmx-users at maillist.sys.kth.se>
Subject: Re: [gmx-users] Tabulated potentials

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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