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

[Marcelo Fabricio Masman]

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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