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].
