[gmx-users] Info regarding restrained minimization, equilibration & production
jalemkul at vt.edu
Thu May 7 14:55:56 CEST 2020
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
Justin A. Lemkul, Ph.D.
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