Hi,
> I have been using sander for years, mostly for classical MD in PBC boxes
> using the Ewald method and never seen something that happened in my last run.
>
> A nucleic acid (RNA) model in aqueous solution, using Ewald etc. was
> subjected to MD at 300K and nothing strange happened during the first 6
> nanoseconds or so. Then, the mobility of the model started to slowly decrease
> which didn't draw my attention first, but after 11 ns, it was already very
> striking. At the end of the 20 ns run, the trajectory looked like during a
> heavily restrained MD - although no restraints were used after the initial
> equilibration 20 ns earlier. The output file showed energy and temperature
> parameters that didn't look strange at all - when you look at the entire
> trajectory it really looks like after a normal dynamics the model slowly
> stopped moving...
....What follows is pure speculation: You might have used a berendsen
thermostat with tight thermal coupling (=small tautp) *and* periodically
removed center of mass (COM) motion. If this is the case, the phenomenon
is called 'flying icecube'. If not, I honestly have no idea.
I hope that helps
best regards
Andreas
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o Wolfgang Andreas Svrcek-Seiler
o (godzilla)
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Received on Thu Nov 24 2005 - 16:53:00 PST
