[gmx-users] Freezing structure's atom

[Hadi Rahmaninejad]

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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