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

[Quyen Vu Van]

Dear Justin,
Thanks for your respond.
What if I mean turn off residues just by remove the non-bonded term and
then gradually adding non-bonded interactions back?
Best regards,
Quyen

On Mon, Oct 22, 2018, 14:11 Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 10/22/18 7:29 AM, Quyen Vu Van wrote:
> > Dear all,
> > sorry for my unclear question,
> > I attached here the quick draw picture of what I am saying, please take a
> > look: https://www.dropbox.com/s/eycsm3qsywhgxjv/model.pdf?dl=0
>
> What you are trying to do is both technically challenging and physically
> questionable. The free energy options allow you to modulate the
> interactions of a [moleculetype] with the remainder of the system; you
> can't easily decompose individual residues of a protein, which is part
> of a single [moleculetype]. You could manually define A- and B- states
> in the topology and there are various tools to do that.
>
> The bigger problem is, even if you accomplish what you seek in terms of
> the technical setup, it's physically unrealistic. As Mark noted, you
> have an unsatisfied valence at the C-terminus of each residue at each
> interval of time. This is not physically real, as amino acids are simply
> transferred between tRNA and onto the growing polypeptide chain. Simply
> "growing" residues onto the chain will not come close to mimicking
> protein synthesis in any meaningful way.
>
> -Justin
>
> > Thank you and best regards,
> > Quyen
> >
> > On Sat, Oct 20, 2018 at 6:27 AM 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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> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
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