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

[Justin Lemkul]

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

==================================================