[gmx-users] Freezing structure's atom

[Hadi Rahmaninejad]

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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