Recommended way to thermostat a system where one covalently-bound component is fully restrained

User discussions
1

GROMACS version: 2024.2
GROMACS modification: No

Hello everyone,

I’m running an MD simulation of a protein covalently bound to a graphene sheet.
The protein and the sheet were parameterized separately, and I bonded them using the intermolecular_interactions directive at the end of the topol.top file:

[ intermolecular_interactions ]
[ distance_restraints ]
8002 9835 1 0 1 0.146 0.147 0.148 1.0

I want the graphene sheet to remain rigid during the simulation, so I generated a position restraint file and applied it to all graphene atoms.

My question is about temperature coupling.
Normally, I use two tc-grps (solute / solvent). But here the solute contains a fully restrained component (the sheet) covalently bound to an unrestrained component (the protein). If I do not assign the sheet to any tc-grps, GROMACS gives the fatal error:

X atoms are not part of any T-coupling groups

I want the sheet to stay immobile, so I’m unsure whether it is better to keep only two temperature-coupling groups (Protein+graphene together, and solvent), or define three groups (Protein / graphene / solvent), even though the graphene is fully restrained.

I’m also concerned that including a completely restrained group together with the protein in the same tc-group may bias the temperature calculation.

What is the recommended way to thermostat a system where one covalently-bound component is fully restrained and should remain rigid?

Thanks in advance for your help!

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I am unsure about how you should proceed in terms of coupling, but if I remember correctly if you use a thermostat then all the atoms of the systems must be part of a coupling group (and only once, no doubles). The silver lining is that if you check the mdp options you see that you can set the coupling constant tau-t to tau-t = -1 to have no coupling in that group. So in case you decide to have it uncoupled then you can split the system atoms into solute/solvent/sheet and assign -1 to the sheet to have no thermostatting on it.

3

Thank you! It seems to be working