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 < [email protected]> 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 > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- ******************************************************* 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: [email protected] e-mail: [email protected]
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