Hello gmx-users, Thanks for the reply Mark.
I was going through the tutorial: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/03_workflow.html, for setting up free energy calculations routine to apply REST2 for my system. I am studying folding of a small peptide on a lipid surface and I am generating replicas through various lambdas. Since I am just scaling the potential via a dual topology file and as such the temperature of the system stays at say 300 K defining fep_lambdas = 0 0.1 0.2 ....... in a single .mdp will not work. However, I can set up various single lambda value (fep_lambdas) in separate directories. ************************************************************************************************************************************************************************************************* The tutorial says the following: ------------------------------ free_energy = yes Indicates that we are doing a free energy calculation, and that interpolation between the A and B states of the chosen molecule (defined below) will occur. ------------------------------ init_lambda_state = 0 In previous GROMACS versions, the "init_lambda" keyword specified a single value of λ directly. As of version 5.0, λ is now a vector that allows for transformation of bonded and nonbonded interactions. With the init_lambda_state keyword, we specify an index (starting from zero) of the vector to be utilized in the simulation (more on this later). ------------------------------ delta_lambda = 0 The value of λ can be incremented by some amount per timestep (i.e., δλ/δt) in a technique called "slow growth." This method can have significant errors associated with it, and thus we will make no time-dependent changes to our λ values. ------------------------------ fep_lambdas = (nothing) You will note that this keyword is not specified. In previous GROMACS versions, the use of init_lambda and foreign_lambda controlled the value of λi and the additional values of λ for which energy differences would be evaluated for configurations at λi. This is no longer the case. One can explicitly set values of λ in the fep_lambdas keyword, but instead we allow the calc_lambda_neighbors keyword (see below) to automatically determine these additional values. ------------------------------ calc_lambda_neighbors = 1 The number of neighboring windows for which energy differences are computed with respect to λi. For instance, if init_lambda_state is set to 10, then energy differences with respect to λ states 9 and 11 are computed during the run with calc_lambda_neighbors = 1. ------------------------------ vdw_lambdas = ... An array of λ values for the transformation of van der Waals interactions. ------------------------------ coul_lambdas = ... An array of λ values for the transformation of Coulombic (electrostatic) interactions. ------------------------------ bonded_lambdas = ... An array of λ values for the transformation of bonded interactions. ************************************************************************************************************************************************************************************ *FEP part of my nvtlambda0.mdp for lambda=0 and init_lambda_state 0 ( complete .mdp attached)* ; Free energy control stuff free_energy = yes init_lambda_state = 0 delta_lambda = 0 fep_lambda = 0 calc_lambda_neighbors = 1 ; only immediate neighboring windows ; Vectors of lambda specified here vdw_lambdas = 0.00 coul_lambdas = 0.00 bonded_lambdas = 0.00 ;not transforming any restrained interactions restraint_lambdas = 0.00 ; Masses are not changing (particle identities are the same at lambda = 0 and lambda = 1) mass_lambdas = 0.00 ; Not doing simulated temperting here temperature_lambdas = 0.00 ; Options for the decoupling ;sc-alpha = 0.5 ;sc-coul = no ; linear interpolation of Coulomb (none in this case) ;sc-power = 1.0 ;sc-sigma = 0.3 couple-moltype = PROA ; name of moleculetype to decouple couple-lambda0 = vdw-q ; all interactions couple-lambda1 = vdw-q ; all interactions couple-intramol = yes nstdhdl = 10 ;output files dhdl-derivatives = yes dhdl-print-energy = potential *I have the following questions:* a) So if I have 10 replicas/lambda values those will correspond to init_lambda_state? b) Now, for lambda value say 0.1, *the init_lambda_state = 1* and fep_lambda=0.1, vdw_lambdas = 0.1, coul_lambdas = 0.1, bonded_lambdas = 0.1 For lambda value say 0.2, the *init_lambda_state = 2* and fep_lambda=0.2, vdw_lambdas = 0.2 , coul_lambdas = 0.2, bonded_lambdas = 0.2 ........and so on .......... c) I do not require to incorporate soft-core interactions because for my system, particles are not growing out of anything/disappearing at any lambda value. Am I correct in my thinking? Kindly guide. Many thanks in advance, sxn On Tue, Aug 23, 2016 at 6:59 PM, Mark Abraham <[email protected]> wrote: > Hi, > > Just as with temperature REM, at the intervals you choose, the simulation > will stop and adjacent replicas will do a Metropolis check for whether > their configurations are representative of the conditions in the other > simulations. The principle is independent of what varies across replicas. > > Mark > > On Wed, Aug 24, 2016 at 12:54 AM shivangi nangia < > [email protected]> > wrote: > > > Dear Mark, > > > > Sorry about posting in the wrong mailing list. > > > > I understand that when implementing REST2 in GROMACS I am generating > > replicas through various lambdas. > > These replicas will run at same temperature say at 300 K and will only > have > > an "effective temperature". > > > > [a-The lambdas will vary from 0 (low T) to 1 (High T), > > b- the charges, epsilon values and k values are scaled in a dual topology > > file] > > > > What I was confused about is will/how there be an "exchange" in these > > replicas? > > > > kindly advice. > > > > > > Many thanks in advance, > > sxn > > > > > > On Tue, Aug 23, 2016 at 6:01 PM, Mark Abraham <[email protected]> > > wrote: > > > > > Hi, > > > > > > Please do not post questions about how to use GROMACS to the > > gmx-developers > > > mailing list, which is for questions about how to write code related to > > > GROMACS. > > > > > > On Tue, Aug 23, 2016 at 8:29 PM shivangi nangia < > > [email protected] > > > > > > > wrote: > > > > > > > Hello, > > > > > > > > I have a question regarding implementing REST2 in GROMACS as > suggested > > > in: > > > > ( > > > > On easy implementation of a variant of the replica exchange with > solute > > > > tempering in GROMACS, J Comput Chem. 32, 1228-1234, 2010). > > > > > > > > > > There's a rather full explanation of what is going on in that paper. I > > > trust you've read and understood it. > > > > > > > > > > How does the gromacs machinery know how to carry out the > > > exchange/swapping? > > > > > > > > > > The Hamiltonian (ie lambda) differs between replicas. > > > > > > > > > > the -replex probably will generate copies of the system at higher > > > > temperature which I do not want. > > > > > > > > > > You're assuming replica exchange means temperature REM, which is not > what > > > that paper is talking about. > > > > > > Mark > > > > > > > > > > Kindly reply. > > > > > > > > Thanks in advance. > > > > > > > > sxn > > > > -- > > > > 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 [email protected]. > > > > > > > -- > > > 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 [email protected]. > > > > > -- > > 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 [email protected]. > > > -- > 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 [email protected]. >
-- 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 [email protected].
