Dear Justin Thank you very much for your prompt reply. I have read about your Perl scripts. Kindly, would you please let me know where did you exactly set that Lambda must increase from 0 to 1 by increment of 0.05? which parameter in your energy stuff stating that Lambda must increase by 0.05 in every step? Best regards Meisam
Message: 3 > Date: Tue, 27 Sep 2011 13:38:54 -0400 > From: "Justin A. Lemkul" <jalem...@vt.edu> > Subject: Re: [gmx-users] Re: problem in binding free energy > calculation and setting Lambda > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <4e820a2e.30...@vt.edu> > Content-Type: text/plain; charset=windows-1252; format=flowed > > > > meisam valizadeh kiamahalleh wrote: > > Dear Marcelo > > > > Thank you very much for you kind reply. > > Actually, I am following Justin Lemuk's tutorial. He used pear script to > > do all simulations in one setting. Unlike him, I want to do each one > > separately and unfortunately, I couldn't get any info for my second > > question which is about setting initial and final Lambda for my energy > > stuff in each simulation. Could you please help me which parameters I > > need to change for each step? > > The Perl scripts write the files you need to complete the tutorial. You > can > then run as many of the resulting Bash scripts to execute the simulation(s) > for > individual lambda values. The theoretical background is all explained in > the > tutorial. You need to do a transformation between lambda = 0 and lambda = > 1, > with sufficient intermediate values to get good overlap of the free energy > histograms (also explained in the tutorial). > > -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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