Hi,
>
> We are running a md on a modified oligo under sander_classic. The run went for 2 ns. After about 1 ns, the total energy of the system started to decrease and the rate of the decrease appears to be accelerating as the run continues. Other quantities (temp, pressure) are constant but the density is increasing with corresponding decrease in volume. The .in file parms are below. I don't really believe that the decrease in
> total energy is real and would like to know it's source and what to do
>about it. Thanks.
this looks like the 'flying icecube'
since I am not familiar with all the options listed in your .out file I
can
not tell whether you told sander to remove the COM motion and rotation
about the COM. But I observed the same phenomenon in my first MD
experiments.
If you have not done it, you should do it next time.
what seems to happen is that verlocity rescaling slowly saps enery from
high
frequency motions and pumps it into the low frequency ones ( i.e. COM
motion, if available)
> tautp = 0.2, tauts = 0.2,
that seems a bit strong (I do not know of a general rule how strong tautp
should be).
hope it helps,
have fun
andreas
--
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o Wolfgang Andreas Svrcek-Seiler
o (godzilla)
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Received on Mon Jul 30 2001 - 02:06:55 PDT
