> > > Message: 1 > Date: Tue, 05 Jul 2011 19:14:04 -0400 > From: "Justin A. Lemkul" <jalem...@vt.edu> > Subject: Re: [gmx-users] free energy calculations > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <4e139abc.1030...@vt.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > > Ragothaman Yennamalli wrote: > > Hi, > > I want to run free energy calculations on a particular protein-ligand > > complex. I do not have much knowledge on this so I have some questions, > > hopefully someone might give me clear answers. > > I am following the tutorial given in this link: > > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/08_advanced.html > > > > My questions are as follows: > > 1. I am assuming that I do not need the "protein without the ligand" > > form for free energy calculations. Am I right? > > > > Free energy calculations can be done on a number of systems. The tutorial > is > just one simple example. >
Thanks for the mail. So, I technically do not need both the un-complexed and complexed form of the protein with the ligand. > > > 2. To use g_bar, I need to run the protein-ligand complex with > > a) first with lambda ranging from 0.5 to 1 for vdw coupling and > > b) followed by lambda ranging from 0.5 to 1 for coulombic coupling > > Adding these would give the deltaG I am looking for. Am I right? > > > > No. The range for lambda should be 0 to 1. Using 0.5 to 1 gives only part > of > the free energy for the transformation, and not necessarily half. > Apologies, I should have mentioned as from 0 to 1. So, the first step is to do vdw coupling followed by coulombic coupling. Right? > > > 3. Are there any papers that use g_bar function in gromacs to calculate > > free energy? > > > > The g_bar tool is relatively new to Gromacs, so maybe not. The BAR method > itself has been around for decades though, so its applications have been > demonstrated in the literature many times. > Thanks for pointing this. Raghu > > -Justin > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== >
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