Hi everybody,
I just ran a number of simulations with two large and roughly spherical molecules in a primitive model electrolyte (epsilon=80), they are constrained to the z-axes and i calculate the PMF using the pull code restraining the distance between the two molecules. integration is done with langevin dynamcs (gmx-4.5.3) what i see is this: I start several runs all with the same initial orientations of the two molecules only the distance varies, the dynamics seems to go well, but when i compare the FINAL ORIENTATIONS of the two molecules after multiple runs at different distances they are NEARLY THE SAME not matter which distance i choose. below is the relevant part of my mdp file: integrator = sd tau_t = 2.0 ref_t = 300 gen_vel = yes gen_temp = 240.0 gen_seed = xxx ; this varies tc_grps = System nsteps = 200000 dt = 0.001 The forces depend on the distance of course (the molecules have a heterogeneous charge distribution) and this is a highly chaotic system therefore the probability that the conformations (basically the rotational DOFs of the two molecules) are the same or very similar after 200 ps at 300K should basically be ZERO ... but this is what i see, its re-producible and happens at different distances AND with different molecular topologies (charge distributions). a possible explanation for this behaviour might be that of the terms in eqn. 3.108 only the velocity dependent and the random term are actually considered but not force term AND gen_seed doesn't make any difference for SD ... then the small differences i see would be only from round-off errors ... ??? has anybody seen something similar ? i'd appreciate any suggestions! thanks Michael
-- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
