[gmx-users] sd simulations

Ran Friedman r.friedman at bioc.uzh.ch
Thu Jun 12 14:20:38 CEST 2008


I'm simulating a system of molecules, made of coarse-grained molecules.
Each molecule has 3 uncharged CG atoms so the interactions are governed
by LJ, bonds and angles. I use SD for the simulations. My problem is
that the LJ energy is not converged in the simulations - it just climbs,
and the particles diverge. I'm not talking about an initial rise in the
energy of a minimised system. Rather, after >100,000 steps the energy
continues to rise. If I use very high friction (small TauT) the effect
is somewhat slower but it's still there.

Any hints about this?


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