[gmx-users] Free energy change with harmonic restraints

[bipin singh]

I think It means that, you can use  "restraint-lambdas" as a vector to
control the restraints (bond, angle dihedral) while using the pull-code and
get the corresponding free energy change (I suppose).


------------------------------
Thanks and Regards,
Bipin Singh

On Fri, Jul 10, 2015 at 12:39 AM, Natalie Nguyen <nguyenn at wittenberg.edu>
wrote:

> Dear Asaf,
>
> Thank you again for putting in the time to respond to me so quickly.
> What I have been trying to do was start from a system that is not
> restrained and grow the restraints onto the ligand, measuring the change in
> free energy of this. The harmonic restraints used are that of the umbrella
> pull code with a force constant of k= 1000 kJ/mol*nm^2. It is mentioned In
> the Gromacs manual for mdp options that the pull code can be controlled
> with "restraint-lambdas", but there is not much detail other than this. I
> imagine that lambda =0 would represent a nonexistent potential with k= 0
> and at lambda = 1 a full strength potential would be imposed.
> Please feel free to ask me to add more detail!
>
> Warm regards,
> Natalie
>
> ________________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of
> asaffarhi at post.tau.ac.il <asaffarhi at post.tau.ac.il>
> Sent: Thursday, July 09, 2015 10:38 AM
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: Re: [gmx-users] Free energy change with harmonic restraints
>
> Dear Natalie,
>
> You are welcome.
> Could you please explain in more detail so maybe I can help?
> Do you want to change the strength of the restraints and measure the
> free energy difference associated with this change?
>
> Thanks. p.s there is also http://arxiv.org/pdf/1307.1620v7.pdf with
> the same equations.
>
> Best regards,
> Asaf
>
> Quoting Natalie Nguyen <nguyenn at wittenberg.edu>:
>
> > Dear Asaf,
> >
> > Thank you for the quick reply!
> >
> > I was wondering if it was possible to use thermodynamic integration
> > to represent growing harmonic restraints aside from using an
> > analytical method.
> >
> > I will cite this article most definitely!
> >
> > Natalie Nguyen
> >
> > ________________________________________
> > From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se
> > <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of
> > asaffarhi at post.tau.ac.il <asaffarhi at post.tau.ac.il>
> > Sent: Thursday, July 09, 2015 7:45 AM
> > To: gromacs.org_gmx-users at maillist.sys.kth.se
> > Subject: Re: [gmx-users] Free energy change with harmonic restraints
> >
> > Dear Natalie,
> >
> > You have in
> >
> > http://xxx.tau.ac.il/pdf/1502.07196v3.pdf
> >
> > exact free energy of harmonic covalent bond and bond angle terms (or
> > restrains). See Eqs. (2) and (3).
> >
> > There are also previous studies in the references there.
> >
> > For the dihedral term I assume it can also be calculated exactly (I
> > might upload it).
> >
> > There is also to think if there are other contributions.
> >
> > If you are using it please cite.
> >
> > Best regards,
> > Asaf
> >
> >
> > Quoting Natalie Nguyen <nguyenn at wittenberg.edu>:
> >
> >> Dear all,
> >>
> >>
> >> I am trying to measure the free energy change associated with
> >> adding/removing harmonic restraints imposed on a ligand that is
> >> attached to a protein. Is there any way to set this up?
> >>
> >>
> >> Thank you ahead of time!
> >>
> >>
> >> Natalie Nguyen
> >> --
> >> 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.
> --
> 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.
>