[gmx-users] Info regarding restrained minimization, equilibration & production
paolo.costa85 at gmail.com
Thu May 7 15:05:58 CEST 2020
Thanks Justin. I will then add manually the constraints on the topology
Il giorno gio 7 mag 2020 alle ore 14:56 Justin Lemkul <jalemkul at vt.edu> ha
> 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
> > 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 A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
> Virginia Tech Department of Biochemistry
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> jalemkul at vt.edu | (540) 231-3129
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Paolo Costa, Ph.D.
Department of Chemistry and Biomolecular Sciences
University of Ottawa
10 Marie Curie, Ottawa, ON K1N 6N5, Canada
Room number: DRO 326 (D'Iorio Hall)
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