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Re: [ESPResSo] analyze pressure and energy problems

From: Markus Deserno
Subject: Re: [ESPResSo] analyze pressure and energy problems
Date: Mon, 15 Jun 2009 13:45:42 -0400
User-agent: Thunderbird (X11/20070801)

Dear İbrahim,

without having looked too much at your specific problem...
...but: In "natural" simulation units, assuming all masses are
essentially the same, the integration time step should not
be 1, rather maybe 0.01.  How many seconds that represents
is a whole different question.  This requires mapping and
depends not only on your masses but also the hard-to-guess
speedup factor which you get from coarse-graining.  It seems
to me that your system might just blow up.



> Hi,
> I attached the scripts I am using..The scripts give no error if I dont
> put analyze commmand..The problem seems to come from the analyze
> command..
> I use Angström for lengths, and use 1 as temperature by dividing
> potential energy coefficients to kbT unit.. But to relate time to fs I
> had to also normalize mass by kbT  so that delt=1 will be equal to 1
> fs. Mass values are about 5x10e4 because of this modification. At
> first  I  thought of using  m*=mass/100 and delt*=delt/10, but because
> of velocity-verlet algorithm (v*delt term) would not give correct
> results I did not use.  Am  I missing something?
> Note: I am using  8 Dual-Core AMD Opteron(tm) Processor 8216 with
> x86_64 GNU/Linux OS.
> Thanks very much..
> ibrahim inanc
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Dr. Markus Deserno
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