AMBER Archive (2005)

Subject: AMBER: My model loses its motion in MD

From: Lukasz Bielecki (bielecki_at_rose.man.poznan.pl)
Date: Thu Nov 24 2005 - 09:06:14 CST

Dear Amber experts,

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...

Maybe somebody is able to make some sense out of it.

Many thanks for your help,

Dr. Lukasz Bielecki
Polish Academy of Sciences, Poznan, Poland
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