[gmx-users] Creating distance restraints between two atoms of different molecules

[Mustafa Tekpinar]

Hi Justin,
Thanks for your reply. I added the following code to my mdp files:

pull                  = yes
pull-coord1-type      = umbrella
pull-coord1-geometry  = distance
pull-ngroups          = 2
pull-coord1-dim       = Y Y Y
pull-coord1-start     = no
pull-coord1-init      = 1.060 ; distance (nm) between two atoms
pull-coord1-groups    = 1 2
pull-group1-name      = BC5_&_C1'
pull-group2-name      = DG3_&_C1'
pull-coord1-k         = 1000 ; kJ mol^-1 nm^-2
pull-coord1-rate      = 0

Best,
Mustafa

On Mon, Oct 28, 2019 at 5:47 PM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 10/28/19 12:43 PM, Mustafa Tekpinar wrote:
> > Hello everybody,
> > I am trying to put a distance restraint between two atoms of different
> > molecules, such as DNA and RNA . I created an index file that contains
> only
> > these two atoms. Then, I called gmx genrestr with this index file. Now, I
> > have an itp file, which includes a distance restraint.
> > However, I have two questions here:
> >
> >     1. In positional restraints, the atoms numbers refers to the numbers
> in
> >     moleculetype section, not to the general gro file ordering. However,
> in
> >     my itp file, the numbers refers to the gro file numbering for both
> of the
> >     atoms. Is this correct?
> >     2. Where should I call this itp file in my topology file?
>
> You should use the pull code to employ the restraint. While you can
> define [distance_restraints] under an [intermolecular_interactions]
> directive at the end of the system .top file, it will limit you in terms
> of domain decomposition and your run will be very slow. Use the pull
> code to apply a biasing potential, instead.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
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> Virginia Tech Department of Biochemistry
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>
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-- 
Mustafa Tekpinar, PhD

Pasteur Institute
25-28 Rue du Dr Roux
75015 Paris, France