[gmx-users] Freezing structure's atom

[Mateusz Bieniek]

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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