> > Message: 1 > Date: Thu, 07 Jun 2012 08:53:22 -0400 > From: "Justin A. Lemkul" <jalem...@vt.edu> > Subject: Re: [gmx-users] Regarding Free Energy calculation tutorial > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <4fd0a442.6000...@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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