[gmx-users] Freezing structure's atom

Hadi Rahmaninejad ha.rahmaani at gmail.com
Thu Mar 21 06:15:03 CET 2019


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.


More information about the gromacs.org_gmx-users mailing list