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

[meisam valizadeh kiamahalleh]

>
> 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?
Thank you very much
Best regards
Meisam

>
> Message: 3
> Date: Tue, 27 Sep 2011 11:36:50 +0200
> From: Marcelo Fabricio Masman <mmasman at gmail.com>
> Subject: Re: [gmx-users] problem in binding free energy calculation
>        and     setting Lambda
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID:
>        <CANaLBhhZJn7gUDufayNep8QdKtXbV_q=V3bsjBgFGsZ=+rYAPA at mail.gmail.com
> >
> Content-Type: text/plain; charset="windows-1252"
>
> Dear Meisam,
> Take a look at Justin Lemkul's tutorial. It's very well explained step by
> step:
>
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/index.html
> Good luck,
> Marcelo
>
> On Tue, Sep 27, 2011 at 10:49 AM, meisam valizadeh kiamahalleh <
> meisam488 at gmail.com> wrote:
>
> > Dear GMX Users
> >
> > I would like to let you know that I have run MD simulation on a Carbon
> > nanotube- drug system.
> >
> > All steps (Energy minimization, Postion restrained, Equilibration with
> NVT
> > and NPT ensembles and finally MD) have been done successfully. Currently
> if
> > would like to calculate binding free energy for the system (drug
> molecules
> > inside Carbon nanotube). Here are my questions at this point;
> >
> > 1.May I know if I must add the free energy stuff to all the mdp files for
> > each steps of (Energy minimization, Position restrained, Equilibration
> with
> > NVT and NPT ensembles and finally MD) and redo all the simulation steps?
> I
> > am wondering because I have seen few people who only edited the final
> MD.mdp
> > file and add the free energy stuff.
> >
> >
> > 2. I know to get the binding energy curve; I need to run several
> > simulations, one for each lambda value.  Hence, I need 21 point from
> > Lambda=0 to 1 to get the smooth curve. To do this, I have to start with
> > initial Lambda =0 as stated in the energy stuff below, in my mdp file.
>  May
> > I know which parameter(s) (init_lambda or foreign lambda or ...) need to
> be
> > changed in my mdp file to do the next simulation and until the last
> > simulation? I mean to go from Lambda=0.0 to the next lambda =0.05, 0.10,
> > 0.15, … and 1.00.
> >
> > The free energy stuff in my mdp file is as below:
> >
> >
> > ; Free energy control stuff
> >
> > free_energy              = yes
> >
> > init_lambda              = 0.00
> >
> > delta_lambda             = 0
> >
> > foreign_lambda           = 0.05
> >
> > sc-alpha                 = 0.5
> >
> > sc-power                 = 1.0
> >
> > sc-sigma                 = 0.3
> >
> >
> > Your kind advice on this matter would be highly appreciated.
> >
> > Best regards
> >
> > Meisam
> >
> > --
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>
>
>
> --
> *******************************************************
> Marcelo F. Masman, Ph.D.
> Department of Molecular Neurobiology,
> Faculty of Mathematics and Natural Sciences,
> University of Groningen.
>
> Nijenborgh 7
>
> 9747 AG Groningen
> The Netherlands
> Tel. +31 50 363 2363
> e-mail: mmasman at gmail.com
> e-mail: M.F.Masman at rug.nl
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