On Jun 23, 2011, at 5:07 AM, Anja Kuhnhold wrote: > I'm simulating a bead-spring polymer model (1600 chains and 10 beads per > chain in a 26.6^3 box with pbc) with LJ and FENE potentials. > I calculate the mean-square-displacement for different temperatures. For > T=0.46 (in LJ units) I expected to get a plateau in the msd curve (glass > transition)- but there is none. The curve for T=0.46 is similar to the one > for T=1.0 (above glass transition) with only a small shift to lower values- > but no plateau.
Why did you expect a plateau at T=0.46 for this system? Is there any published literature out there for your system? Also, keep in mind that many people wouldn't call a plateau in the rmsd curve a glass transition. > My .mdp-files look as follows: > > integrator = md-vv > dt = 0.0035 > nsteps = 100 > nstxout = 1 > nstvout = 1 > nstfout = 1 > nstlog = 1 > ns_type = grid > pbc = xyz > periodic_molecules = yes > rvdw = 1.12 > rlist = 1.3 > tcoupl = nose-hoover > tc-grps = System > tau_t = 20 > ref_t = 55.32 > vdwtype = Shift > rcoulomb = 1.12 > coulombtype = Reaction-Field-zero > epsilon_rf = 0 > Is the ref_t correct? That depends on the interaction energy you specified in the force field parameter file. > The results in the md.log file say T is about 89. Oh, that's weird. Are you sure your system is equilibrated? Hope this helps, Lutz -- 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
