[gmx-users] Tabulated potentials

[Ali Khodayari]

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.

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
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before 
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users 
> > or send a mail to gmx-users-request at gromacs.org.
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before 
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or 
> send a mail to gmx-users-request at gromacs.org.
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before 
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or 
> send a mail to gmx-users-request at gromacs.org.
--
Gromacs Users mailing list

* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.