[gmx-users] Freezing structure's atom

[Mateusz Bieniek]

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
> >> --
> >> Gromacs Users mailing list
> >>
> >> * Please search the archive at
> >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> >> posting!
> >>
> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>
> >> * For (un)subscribe requests visit
> >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> >> send a mail to gmx-users-request at gromacs.org.
> >>
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.