Re: [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  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
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==
>
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-- 
Mustafa Tekpinar, PhD

Pasteur Institute
25-28 Rue du Dr Roux
75015 Paris, France
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[gmx-users] Creating distance restraints between two atoms of different molecules

[Mustafa Tekpinar]

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?


Thanks in advance for your help,
Mustafa


-- 
Mustafa Tekpinar, PhD

Pasteur Institute
25-28 Rue du Dr Roux
75015 Paris, France
-- 
Gromacs Users mailing list

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[gmx-users] Running jobs between different Gromacs versions

[Mustafa TEKPINAR]

Hi,
I was wondering if it is correct to prepare a Gromacs simulation with
Gromacs 4.5.5 until production run and to do the production (starting from
final tpr file) with Gromacs 5.0.

Thanks in advance,
Mustafa Tekpinar
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