[gmx-users] Re: gmx-users Digest, Vol 98, Issue 44

[neeru sharma]

>
> Message: 1
> Date: Thu, 07 Jun 2012 08:53:22 -0400
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] Regarding Free Energy calculation tutorial
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4FD0A442.6000107 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> On 6/7/12 8:26 AM, neeru sharma wrote:
> > Dear Justin,
> >
> > Greetings of the day!!
> >
> > I am following your tutorial for the calculation of free energy change
> in gromacs.
> >
> > It says about the change in state A and state B. I have a query
> regarding these
> > states. What are the 2 states A and B in the tutorial and how can I
> define these
> > 2 states for my system?
> >
>
> The changes applied between state A and B are defined in the .mdp file
> based on
> the couple-lambda0 and couple-lambda1 settings.  These are used to
> transform
> either vdW or Coulombic interactions.  If you need to make some other type
> of
> change (i.e. a mutation), then you would do so in the topology, setting
> B-state
> parameters explicitly.
>
> > For example, I have a Protein-Mg-GTP complex (In initial state A, 2
> specific
> > H-bonds are absent and in the final state, these 2 H-bonds are present).
> So, how
> > can I implement this for the calculation of change in free energy to my
> system?
> >
>
> This doesn't sound like something that can be done with the decoupling
> technique; it sounds to me more like a structural change.  Perhaps you can
> do
> some careful calculations using the pull code, but it is not clear to me
> what
> you are trying to do.
>
> -Justin
>
> --
> ========================================
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
>
Thanks for the reply.
Well,yes it is more of the strutural change in case of my case which can
also be quantified in terms of presence and absence of these 2 H-bonds. And
as the two structures are distinct from each other too, there has to be
some energy change which I want to calculate too. Moreover, this structure
change and the appearance of these H-bonds take long time and cross a
energetic barrier too, I am trying to calculate this energy barrier too.
Regarding the pull code, I will also try it for my system

---
Neeru
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