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 <jalem...@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 > 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 > > ================================================== > > -- > 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-requ...@gromacs.org. > -- Mustafa Tekpinar, PhD Pasteur Institute 25-28 Rue du Dr Roux 75015 Paris, France -- 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-requ...@gromacs.org.
