Very custom constraints issue

User discussions
1

GROMACS version: 2022
GROMACS modification: No

I want to simulate a system containing a protein, water, and some solutes (urea and TMAO). I have the following constraints (for LINCS) situation: the protein should have only h-bonds constrained, the urea should be totally constrained, while the TMAO should be totally unconstrained (even C-H bonds). Is there a way I can do this without manually putting constraints in the [constraints] section of the topology for all the species?

Thank you!
Dan

2

No, unfortunately there is no other way of doing this.

3

Actually, you can use a trick to be able to specify h-bonds constraints, so don’t need to change anything for the protein, which I assume would be the most work. You change TMAO to use (H-)bonds type 6 instead of 1, so these are not converted to constraints by grompp. But then you need to manually set all exclusions in TMAO.