[gmx-users] Tabulated potentials

Alessandra Villa alessandra.villa.biosim at gmail.com
Wed Feb 19 09:12:39 CET 2020


Hi,

On Tue, Feb 18, 2020 at 12:12 PM Ali Khodayari <
ali.khodayari at student.kuleuven.be> wrote:

> So I am using Iterative Boltzmann Inversion to get the CG potentials for a
> cellobiose-water solution. During the first step of the simulation by
> gromacs, I get the error, which I think it might be due to some large
> forces, causing the distance between the CG beads to increase to values
> more than the length of the table.  The bonded tables have values in
> between 0 to 0.5 nm for r.
>

As far as I recall the error messages that you got was something like

"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"

Your table is up to the 0.5 (501 lines), but the program is looking for a
values of 0.575410 nm, that it is out of the range of the values for your
table. Could it be that one of cellobiose-water distances  is 0.575410 nm
in the first frames?
The errors  seems to indicate that you need a longer table at least up 0.58
nm or more (even if it corresponds to high potential values).

Note that if  your table is  for  non-bonded interactions, then also the
mdp parameters set requirement on the table lengths

(see
http://manual.gromacs.org/documentation/current/user-guide/mdp-options.html?highlight=table#tables
)

Best regards
Alessandra


> 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: maandag 17 februari 2020 9:34
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Tabulated potentials
>
> 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/topol
> > ogies/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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