[gmx-users] Info regarding restrained minimization, equilibration & production

Justin Lemkul 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 
non-sequential atoms.



Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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