[gmx-users] Re: problem in binding free energy calculation and setting Lambda

[meisam valizadeh kiamahalleh]

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" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] Re: problem in binding free energy
>        calculation and setting Lambda
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4E820A2E.30501 at 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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