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

[Justin Lemkul]

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

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Justin A. Lemkul, Ph.D.
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jalemkul at vt.edu | (540) 231-3129
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