[gmx-users] Freezing structure's atom

[Hadi Rahmaninejad]

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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