[gmx-users] plateau in msd (glass transition); ref_t
Lutz Maibaum
lutz.maibaum at gmail.com
Tue Jun 28 03:35:30 CEST 2011
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
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