[gmx-users] Tabulated potentials

[Alessandra Villa]

Hi,
On Fri, Feb 14, 2020 at 5:17 PM Ali Khodayari <
ali.khodayari at student.kuleuven.be> wrote:

> 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
>
>
Where exactly did you get this error?

It looks like that your table is not covering all the request values (that
means that it is too short) or
the file is missing same values.

Best regards
Alessandra



> 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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