[gmx-users] defining parameters in a separate itp file

[Dave M]

Hi Justin,

Thanks for your reply but am getting error suggesting a intermolecular
chemical bond is not allowed:

Program:     gmx grompp, version 2016.4

Source file: src/gromacs/gmxpreprocess/convparm.cpp (line 649)

Fatal error:

The intermolecular_interaction can not contain chemically bonding
interactions

[ molecules ]

; name        number

molA 1

molB 1

W  2420


[intermolecular_interactions]

 [ bonds ]

    1     158     1  0.4  2000

This is coarse-grained model and as a simple test I used global atom
numbers between two water single particles (intermolecular) but I get the
same error.

regards,
Dave

On Mon, Oct 28, 2019 at 5:58 AM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 10/27/19 9:24 PM, Dave M wrote:
> > Hi All,
> >
> > I am trying to define a bond between two molecules. Their parameters are
> > defined in separate itp files: molA.itp and molB.itp. I know I can
> > combine both the itp files but I am just wondering if I can define extra
> > bonds/angles joining two molecules in a separate itp file taking care of
> > atom numbers. To test it I defined an extra bond joining two atoms
> (elastic
> > bond) from two molecules in a separate bond.itp file but it does not look
> > like molecules come close at all.
> > Not sure this is a correct way. And, also is there a way I can print the
> > bond parameters from tpr file to confirm whether all the bonds and angles
> > are read from itp files.
> >
> > My top file looks like this
> >
> > #include "mol1.itp"
> >
> > #include "mol2.itp"
> >
> > #include "bond.itp"
> >
> >
> > [ system ]
> >
> > test
> >
> >
> > [ molecules ]
> >
> > ; name        number
> >
> > molA 1
> >
> > molB 1
>
> You don't even need a separate .itp file. After you define [molecules],
> you can add an [intermolecular_interactions] directive like so:
>
> [intermolecular_interactions]
> [bonds]
> atom_i atom_j b0 kb
>
> Note that atom_i and atom_j, unlike individual [moleculetype]
> definitions, refer to the global atom numbers in the coordinate file.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==================================================
>
> --
> 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.
>