Hi all,
I want to constrain 2 atoms in my molecule. For that I created the indeces with gmxmake and the pose.file with gmxrestr. Right now I wonder, how I should “acitivate” the constraints in the map, beaucse the option constraint = all-atoms works constrains all atom, right? And do I have to set up a constraint-algorithm?
You mean gmx genrestr? This command generates restraints, not constraints (make sure you know the difference between these two).
In a Gromacs topology file, the preprocessor allows you to use a syntax like
#ifdef MY_KEYWORD
#include "myposresfile.itp"
#endif
and then myposresfile.itp will be included in that site if your .mdp file contains
define = -DMY_KEYWORD ; (that's not a typo, the -D is needed)
which is useful if you want to include or exclude some sections based on your .mdp settings.
Of course, instead of writing #include "myposresfile.itp" you can literally paste the content of that file - works the same, except this way you don’t need to move this file around as a dependency before running gmx grompp.
Thank you for you response, but in the .mdp-file, do I need to put the actual name for the -DMY_KEYWORD e.g. -DCLAHIS_posre.itp?
No, in the .mdp file, the define statement only defines/sets certain keywords/statements. These do not correspond to specific restraint files or anything like that. In the example provided above,
-DMY_KEYWORD should just correspond to MY_KEYWORD in the #ifdef statements in the topology file (or its included .itp files). The #include "myposresfile.itp" is where you should specify the file name of the file containing the restraings, e.g., CLAHIS_posre.itp. https://manual.gromacs.org/current/user-guide/getting-started.html#topology-include-file-mechanism might shed some more light on this.