[gmx-users] plateau in msd (glass transition); ref_t

[Lutz Maibaum]

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