> > 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 <[email protected]> > Subject: Re: [gmx-users] problem in binding free energy calculation > and setting Lambda > To: Discussion list for GROMACS users <[email protected]> > Message-ID: > <CANaLBhhZJn7gUDufayNep8QdKtXbV_q=V3bsjBgFGsZ=+ry...@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 < > [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] > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20110927/9a19820e/attachment-0001.html > > ------------------------------ > > -- > 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! > > End of gmx-users Digest, Vol 89, Issue 145 > ****************************************** >
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