[gmx-users] problem in binding free energy calculation and setting Lambda
Marcelo Fabricio Masman
mmasman at gmail.com
Tue Sep 27 11:36:50 CEST 2011
Take a look at Justin Lemkul's tutorial. It's very well explained step by
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
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Marcelo F. Masman, Ph.D.
Department of Molecular Neurobiology,
Faculty of Mathematics and Natural Sciences,
University of Groningen.
9747 AG Groningen
Tel. +31 50 363 2363
e-mail: mmasman at gmail.com
e-mail: M.F.Masman at rug.nl
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