Hi, You certainly want the code to take the path where lambda varies, but if you comment out the check for unequal lambda and avoid the check that T is unequal, things should work fine.
Mark On Thu, Mar 8, 2018 at 2:59 AM Carlo Martinotti < carlo.martino...@postgrad.curtin.edu.au> wrote: > Hello everybody, > > So i am trying to set up a replica exchange with solute tempering > simulation for my membrane-drug systems. We modified the gromacs source > code in a way that allows the modification of the hamiltonian of singular > pairs of interactions (eg solute-water, solute-solute, ion-solute etc). > Until now I tested this part on single simulations and it's now working as > intended. Now though i have to switch on the replica exchange part and > allow them to exchange. > Right now i tried to set up a test system with 2 replicas at the same > temperatures, but with different scaling. > Again, remember this is an in house modification of the code, not the > classical REST methodology. > I launch the classical mdrun -multidir -replex and the system is > complaining that there is nothing to exchange cause the systems are the > same. I assume that this is because the temperature of two systems are > actually the same and he is using equation 3.141 from manual 4.6.7 part > 3.13. > > So here is my question: > > From my understanding of manual 4.6.7 part 3.13, to allow the exchange as > per equation 3.142 i MUST use the lambda routine. My idea is then to try to > trick the program inserting the same values of lambdas in both of the > replicas so to force gromacs tu use the equation 3.142 for the evaluation > of the probability of exchange. > I am pretty sure that the program is going to complain about that, but in > the case i can eliminate the check for identical lambdas in the source code. > > Do you think this would suffice? Or do you see things that i am missing > out ? > > Of course i know that without knowing what exact tweaks of the code we did > you can't answer accurately, but assume that when a single tempered > simulation is run the functions to compute the forces and the vdw terms are > changed in the beginning of the simulations and they stay changed for the > whole of the simulation, so that when gromacs will compute the cross terms > in ((U1(x2) − U1(x1)) + (U2(x1) − U2(x2)) it should be assumed to use the > right hamiltonian. > > Thanks in advance for the time and effort! > > -- > 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.