Hi all, I¹m performing free energy calculations based on Crooks Fluctuation Theorem. To do this I¹ve used PMX to implement a dual topology. To keep things simple, it is a transmembrane polyleucine helical protein where one leucine is transforming into a serine - then there is the backward transition of serine into Leucine, required for the overlap of two gaussian distributions (forward and backward).
I have a very complicated arrangement of steps to equilibrate the system, in very brief I have only included those involved once the protein is embedded in the bilayer (bilayer eq was around 40 ns over various stages). For a backward eq (serine->leucine) I used the parameters: free_energy = yes init_lambda = 1 ;0=forward 1=backward delta_lambda = 0 ;equilibrium nstdhdl = 1 sc-coul = yes sc-alpha - 0.3 sc-sigma = 0.25 sc-power = 1 And the eq steps: -Steepest descent (<100 kjmol threshold) -NVT 100ps (carbon-alpha posres 1000 kjmol) -NPT 100ps (carbon-alpha posres 1000 kjmol - Berendsen pressure) -NPT 10ns (carbon-alpha posres 1000 kjmol - PR pressure) -NPT 2.5 ns (turn OFF posres) The above steps produce a system with serine in the polyleu. I then discard the first 1.5 ns and take 10 sets of coordinates and velocities from the last 1ns. This is for my Œfast¹ backward (serine->leucine) 100 ps transformation using the MDP parameters: free_energy = yes init_lambda = 1 ;0=forward 1=backward delta_lambda = -0.00002 ;transitions nstdhdl = 1 sc-coul = yes sc-alpha - 0.3 sc-sigma = 0.25 sc-power = 1 When I run the 10 Œfast¹ transition production runs approximately half of them immediately result in the error: Step 5: The charge group starting at atom 63445 moved more than the distance allowed by the domain decomposition (1.420000) in direction Z distance out of cell 70.681579 Old coordinates: -48.465 256.312 81.655 New coordinates: -48.465 256.312 81.655 Old cell boundaries in direction Z: 5.728 10.974 New cell boundaries in direction Z: 5.728 10.974 ------------------------------------------------------- Program mdrun_mpi_d, VERSION 5.0 Source code file: /home/sacat2/gromacs_source/gromacs-5.0/src/gromacs/mdlib/domdec.c, line: 4380 Fatal error: A charge group moved too far between two domain decomposition steps This usually means that your system is not well equilibrated For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- I understand what this error means, but I was wondering whether I was doing something far more fundamentally wrong, given that every forward transition (same eq set up, just using init_lambda = 0 and delta_lambda = 0.00002) never produce this error! They always work, and monitoring my work gives me an amazing gaussian distribution. I have put the 2.5ns production run with no position restraints up for a further 2.5 ns, and I¹m testing whether frames from the last ns produce similar errors i.e., does the inclusion of serine require further equilibration. I would appreciate any thoughts. Many thanks Anthony -- 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.