GROMACS version: 2023.3
GROMACS modification: No
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I am running a MARTINI course-grained simulation and the reported topologies have most beads linked by harmonic bonds. However, in some cases, the CG beads are not linked by harmonic bonds but type 1 [ constraints ] or type 10 [ bonds ] (restraint potential) are applied. The force constants for interbead bonds and constraints are 20000-50000. I was wondering what is the criteria for choosing type 1 constraints or type 10 bonds over harmonic bonds.
Similarly, the bond angles are also expressed as type 2 or type 10. How are they chosen?
Thanks in advance for help.
Regards,
Raman
One thing I see about constraints in Martini topologies (for proteins) is that they are embedded in a conditional block, so by defining a FLEXIBLE keyword in the .mdp you can swap between having side chains connected by harmonic bonds or rigid constraints. I’m not sure about the relative merits of both for practical applications though.
On the use of type 10 restraint potentials, you should probably read that in Martini papers or talk to Martini developers, as they maintain the scripts that assign these parameters, and Gromacs files for residue definitions. I guess the application of this interaction type is specific to a subgroup of residues so it’s hard to provide a general answer.
Thanks for the reply. Seems like I need to dig deeper.