[gmx-users] Re: gmx-users Digest, Vol 98, Issue 44
neeru.bioinfo at gmail.com
Thu Jun 7 16:31:09 CEST 2012
> 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
> either vdW or Coulombic interactions. If you need to make some other type
> change (i.e. a mutation), then you would do so in the topology, setting
> parameters explicitly.
> > For example, I have a Protein-Mg-GTP complex (In initial state A, 2
> > 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
> 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
> some careful calculations using the pull code, but it is not clear to me
> you are trying to do.
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
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
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