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

[Amir Zeb]

alright Mark,

Thanks a lot


On Tue, Dec 20, 2016 at 3:00 AM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> 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
> > > > --
> > > > Gromacs Users mailing list
> > > >
> > > > * Please search the archive at
> > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > > posting!
> > > >
> > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > >
> > > > * For (un)subscribe requests visit
> > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or
> > > > send a mail to gmx-users-request at gromacs.org.
> > > >
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at http://www.gromacs.org/
> > > Support/Mailing_Lists/GMX-Users_List before posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > > * For (un)subscribe requests visit
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > > send a mail to gmx-users-request at gromacs.org.
> > >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>