[gmx-users] Free energy change with harmonic restraints

[Natalie Nguyen]

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
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