[gmx-users] Freezing structure's atom

Mateusz Bieniek bieniekmat at gmail.com
Thu Mar 21 15:43:17 CET 2019


There a "gmx make_ndx" command to make .ndx group. They ahve their names.
And it needs to be inserted in there.

Please have a look at the .ndx file to see what it does. For any name it's
just a list of atoms.


On Thu, 21 Mar 2019 at 14:39, Hadi Rahmaninejad <ha.rahmaani at gmail.com>
wrote:

> Sorry I forgot to ask this question: did you determine "slab" group in your
> .gro file?
>
> On Thu, Mar 21, 2019 at 10:29 AM Hadi Rahmaninejad <ha.rahmaani at gmail.com>
> wrote:
>
> > Hello Mateusz,
> >
> > Thank you for your help. However, still I am a little confused. suppose
> > that this is the .mdp file for minimization:
> > integrator  = steep         ; Algorithm (steep = steepest descent
> > minimization)
> > emtol       = 1000.0        ; Stop minimization when the maximum force <
> > 1000.0 kJ/mol/nm
> > emstep      = 0.01          ; Minimization step size
> > nsteps      = 50000         ; Maximum number of (minimization) steps to
> > perform
> >
> > ; Parameters describing how to find the neighbors of each atom and how to
> > calculate the interactions
> > nstlist         = 1         ; Frequency to update the neighbor list and
> > long range forces
> > cutoff-scheme   = Verlet    ; Buffered neighbor searching
> > ns_type         = grid      ; Method to determine neighbor list (simple,
> > grid)
> > coulombtype     = PME       ; Treatment of long range electrostatic
> > interactions
> > rcoulomb        = 1.0       ; Short-range electrostatic cut-off
> > rvdw            = 1.0       ; Short-range Van der Waals cut-off
> > pbc             = xyz       ; Periodic Boundary Conditions in all 3
> > dimensions"
> >
> > Now I need to freez some atoms that I have their index in a file like
> > freez.ndx. How should I change this mdp file? In other word, which
> option I
> > should add to this file?
> >
> > Thank you once more,
> > Hadi
> >
> > On Thu, Mar 21, 2019 at 8:42 AM Mateusz Bieniek <bieniekmat at gmail.com>
> > wrote:
> >
> >> Hi Hadi,
> >>
> >> You can freeze atoms in any simulation, so yes in nvt.mdp or any other
> >> .mdp. That is also why the freezegrps in the URL I attached is in the
> >> section called mdp-options.
> >>
> >> When you run grompp to create the .tpr run file, it will not recognize
> the
> >> group "slab" so you will have to give it the index file: "gmx grompp ...
> >> -n myindex".
> >>
> >> It might be a good idea to consider doing some tutorial with gromacs:
> >> https://www.youtube.com/watch?v=kzJR2_XHkcM
> >> http://www.mdtutorials.com/gmx/
> >>
> >> Best, Mat
> >>
> >> On Thu, 21 Mar 2019 at 05:15, Hadi Rahmaninejad <ha.rahmaani at gmail.com>
> >> wrote:
> >>
> >> > Hello Mateusz,
> >> >
> >> > First of all, I don’t know where should I use these these commands,
> >> should
> >> > I use for instance in equilibration input file like nvt. mdp file?
> >> Second,
> >> > in which file I should include ndx file? Could you please provide me
> an
> >> > example?
> >> >
> >> > Thank you,
> >> > Hadi
> >> >
> >> > Sent from my iPhone
> >> >
> >> > > On Mar 20, 2019, at 4:07 PM, Mateusz Bieniek <bieniekmat at gmail.com>
> >> > wrote:
> >> > >
> >> > > Hi Hadi,
> >> > >
> >> > > To freeze atoms you have to first create the right group in your
> index
> >> > file
> >> > > .ndx. Then, you use this:
> >> > >
> >> > > freezegrps               = slab
> >> > > freezedim                = Y Y N
> >> > >
> >> > > Where the Ys refer to X Y Z, meaning here the slab group is frozen
> in
> >> X Y
> >> > > dimension but not Z dimension.
> >> > >
> >> > > Please not that the pressure calculation breaks down when freezing
> >> atoms.
> >> > > In that case, they should be excluded from the pressure calculation
> -
> >> > > however this has not been implemented for a couple of years now in
> >> Verlet
> >> > > algorithm.
> >> > >
> >> > > For reference:
> >> > >
> >> >
> >>
> http://manual.gromacs.org/documentation/current/user-guide/mdp-options.html#mdp-freezegrps
> >> > >
> >> > >
> >> > > On Wed, 20 Mar 2019 at 15:55, Hadi Rahmaninejad <
> >> ha.rahmaani at gmail.com>
> >> > > wrote:
> >> > >
> >> > >> Hello dear Gromacs users,
> >> > >>
> >> > >> I know how to restrain atoms of an structure solvated in water with
> >> > force
> >> > >> with option "-DPOSRES". However, for my simulation, I need to
> exclude
> >> > >> position changing from the simulation, in other words, I need to
> >> exactly
> >> > >> fixed them. I highly appreciate if any of you can help me with
> this.
> >> > >>
> >> > >> Thank you in advance,
> >> > >> Hadi
> >> > >> --
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