Apply constraints to desire molecules

User discussions
,
1

GROMACS version: 2021.7
GROMACS modification: Yes/No
Dear all,

I plan to simulate a mixture of octane and CO₂ using different force fields. In my setup, the bonds in octane should be constrained, while the bonds in CO₂ should remain flexible. How can I apply constraints only to octane molecules? From my understanding of the manual, it seems that constraints are applied to all bonds globally rather than to specific molecules.

I would appreciate any guidance on how to achieve this.

Best regards,
Neda

2

Hi,
you could define the contraint in the topology file of octane under the [ moleculetype ] directives. See more details on the syntax here.

You find an example of topology toward the end of the page.
I hope it helps
Alessandra

3

Thank you very much for your help. By using [constraints] in topology file, it is possible to have fixed bonds for desire molecules. Is it also possible to define constraints for angles in topology file?

4

Hi,
It depends what exactly you need. For angle you could use angle restraints or it might also work

contraint with function-type 2

Alessandra