[gmx-users] how to compute charged carried by a single residue

[Mark Abraham]

Hi,

On Tue, Dec 20, 2016 at 9:20 PM Amir Zeb <zebamir85 at gmail.com> wrote:

> Thanks Mark for your quick response,
>
> I did as you mentioned, what i got was actually the total charge of the
> each residue remained constant at the end.
>

Your topology isn't changing over the simulation, so you shouldn't expect
it to change.

What i'm interested in, is that i have to analyze my results and it seems
> that there is loss of electrostatic interaction for a mutated residue but i
> don't know how to calculate this loss.
> Please let me know if you have kindly meet my question?/
>

Your force field does not permit such a decomposition to be meaningful.
There are ways to compute a change in free-energy of binding upon such a
mutation

Mark

Thanks Mark.
>
> Amir
>
> On Tue, Dec 20, 2016 at 2:14 AM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>
> > Hi,
> >
> > You open your topology file in a text editor and see what it is :-)
> >
> > Mark
> >
> > On Tue, Dec 20, 2016 at 9:12 PM Amir Zeb <zebamir85 at gmail.com> wrote:
> >
> > > Hello All,
> > >
> > > I want to know the total charge carried by a specific residue during or
> > > after simulation. Please let me know how may I do it? I don't know the
> > > exact command line
> > >
> > > Thanks
> > > --
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