[gmx-users] NVE simulations
Nguyen Hoang Phuong
phuong at theochem.uni-frankfurt.de
Fri Jul 12 17:21:04 CEST 2002
> Here is a summary in regards to the problems that I experienced with energy
> drift in the microcanonical ensemble. The problem was due to SHAKE. When
> I reduced the time step down to 1fs, the total energy of the system
> *increased*. So now the behavior of my system in the microcanonical
> ensemble turned 180 degrees. I assume from this that it is not a good idea
> to run SHAKE at all in the microcanonical ensemble, as heat may be
> transferred unexpectedly. At least when it is coupled to a heat bath, the
> problem goes away, since you want heat transfer anyway. The dummy atom
> method suggested by Anton is a better approach to increasing the time step
> in NVE simulations.
> Finally, when I implemented a flexible model of CCL4 (no constraints at
> all), there was no energy drift as expected.
unfortunately, it doesn't help for me. I simulate the peptide in spc water
and using NVE ensemble. The LJ potential is replaced by Shift and the PME is employed.
The time step is 0.4fs (0.2fs, 0.6fs,0.8fs,1fs,1.2fs...2fs are tried). Double precision is
switched on, constrains or without constrains are used (tried for both
LINCS and SHAKE). However, after 5ps, the total energy is increased about
10KJ/mol (Initial energy is -17046KJ/mol. Considering the energy drift is
too much, I'm wondering how should I do. Anyone have any ideal?
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