[gmx-users] Turn on/off residues in gromacs

[Dallas Warren]

Could probably do something like that using the
http://manual.gromacs.org/documentation/2018.3/user-guide/mdp-options.html#free-energy-calculations
settings.  Would need to do in blocks though, with manual changes
required in the topology after each section of turning on/off
interactions as you go along.  Whether it would do something sane is
something else entirely though.

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a nail.
On Sat, 20 Oct 2018 at 15:27, Quyen Vu Van <vuqv.phys at gmail.com> wrote:
>
> Dear Mark,
> I mean that e.g my protein has 10 residues in pdb file but at t=0, Gromacs
> will only calculate the interactions of all atoms in residue 1
> t= 1ns (for example) Gromacs will calculate the interactions of all atoms
> in residues 1 and 2, and so on till t= XXX ns, interactions of all atoms of
> full protein is take into account.
> Best regards,
> Quyen
>
>
> On Fri, Oct 19, 2018, 18:42 Mark Abraham <mark.j.abraham at gmail.com> wrote:
>
> > Hi,
> >
> > What do you mean by turning a residue off? What would terminate the
> > chemical bond to the residue that it was bound to?
> >
> > Mark
> >
> > On Fri, Oct 19, 2018, 14:40 Quyen Vu Van <vuqv.phys at gmail.com> wrote:
> >
> > > Dear Gromacs community,
> > > How can I turn off/on residues in the protein, I want to mimic the
> > process
> > > of protein synthesis.
> > > Thank you and best regards,
> > > Quyen
> > > --
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