[gmx-users] Hamiltonian replica exchange in gromacs 4.6.7

Carlo Martinotti carlo.martinotti at postgrad.curtin.edu.au
Thu Mar 8 02:59:26 CET 2018

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!

More information about the gromacs.org_gmx-users mailing list