On 5/7/20 8:53 AM, Paolo Costa wrote:
Dear Justin

that means when I generate the topology file by pdb2gmx I will add manually
the section [constraints] on it?

I suggest you look into the manual to understand different ways of applying constraints. You can either convert bonds into constraints via the "constraints" .mdp option, in which case the force constants are irrelevant but the equilibrium lengths matter, or you do not define any bonds and manually write in the [constraints]. It depends on how you need to treat the system. I know nothing about POMs so I can't comment specifically. If the species is treated as a fully rigid entity (not something GROMACS is really well suited for), then you should probably be writing the topology manually because you will have lots of bonds to non-sequential atoms.

-Justin

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Justin A. Lemkul, Ph.D.
Assistant Professor
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Virginia Tech Department of Biochemistry
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