[gmx-users] lambda value for free energy calculation
Hi all I have aquestion about free energy calculation as in tutorial be said if we want to consider coloumbic interaction we must define lambda as follows: vdw_lambdas = 0.00 0.05 0.10 ... 1.00 1.00 1.00 ... 1.00 coul_lambdas = 0.00 0.00 0.00 ... 0.00 0.05 0.10 ... 1.00 if I want to consider bonded interaction should I write: vdw_lambdas = 0.00 0.05 0.10 ... 1.00 1.00 1.00 ... 1.00 1.00 1.00 1.00 ... 1.00 coul_lambdas = 0.00 0.00 0.00 ... 0.00 0.05 0.10 ... 1.00 1.00 1.00 1.00 ... 1.00 bonded_lambdas=0.00 0.00 0.00 ... 0.00 0.00 0.00 0.00 ... 0.00 0.00 0.05 0.10 ... 1.00 when should we consider temperature_lambdas, mass_lambdas,restraint_lambdas? Thank you very much for your help Regards Azadeh -- This email was Anti Virus checked by Security Gateway. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] lambda value for free energy calculation
>when should we consider temperature_lambdas, mass_lambdas,restraint_lambdas? If hamiltonian of the system changes between initial and final states the corresponding part is given in coul-lambdas vdw-lambdas bonded-lambdas restraint-lambdas mass-lambdas temperature-lambdas change the external conditions (state of the thermostat) and used only for simulated tempering ( http://manual.gromacs.org/documentation/2018-rc1/user-guide/mdp-options.html#free-energy-calculations ) -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] lambda value for free energy calculation
Hi, Did you understand why the tutorial recommended turning on VDW before coulomb? Does that reasoning apply to other interactions? Mark On Tue, Jan 9, 2018 at 5:33 AM wrote: > Hi all > > I have aquestion about free energy calculation > > as in tutorial be said if we want to consider coloumbic interaction we > must define lambda as follows: > > vdw_lambdas = 0.00 0.05 0.10 ... 1.00 1.00 1.00 ... 1.00 > > coul_lambdas = 0.00 0.00 0.00 ... 0.00 0.05 0.10 ... 1.00 > > if I want to consider bonded interaction should I write: > > vdw_lambdas = 0.00 0.05 0.10 ... 1.00 1.00 1.00 ... 1.00 1.00 1.00 1.00 > ... 1.00 > > coul_lambdas = 0.00 0.00 0.00 ... 0.00 0.05 0.10 ... 1.00 1.00 1.00 1.00 > ... 1.00 > > bonded_lambdas=0.00 0.00 0.00 ... 0.00 0.00 0.00 0.00 ... 0.00 0.00 0.05 > 0.10 ... 1.00 > > when should we consider temperature_lambdas, > mass_lambdas,restraint_lambdas? > > Thank you very much for your help > > Regards > > Azadeh > > -- > This email was Anti Virus checked by Security Gateway. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] lambda value for free energy calculation
Hi Dr.Abraham Thank you very much for your answer excuse me but, I didn't understand I want to calculate free energy of drug in water and I want to consider VDW,coulombic and bonding interation with these lambda value vdw_lambdas = 0.00 0.05 0.10 ... 1.00 1.00 1.00 ... 1.00 1.00 1.00 1.00 ... 1.00 coul_lambdas = 0.00 0.00 0.00 ... 0.00 0.05 0.10 ... 1.00 1.00 1.00 1.00 ... 1.00 bonded_lambdas=0.00 0.00 0.00 ... 0.00 0.00 0.00 0.00 ... 0.00 0.00 0.05 0.10 ... 1.00 I think I don't need mass , temperature and restraint value , however I don't know application of them exactly probably when temperature and mass change ,we use those lambda value and when we have a restraint in system we use restraint lambda value. excuse me for elementary question I'm beginner with Gromacs Thank you very much for your help Regards Azadeh -- This email was Anti Virus checked by Security Gateway. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
