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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 2.0.0.6 (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.
Best,
MD
> 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
Associate Professor of Physics ++1-412-268-4401 (office)
Carnegie Mellon University ++1-412-681-0648 (fax)
5000 Forbes Avenue ++1-412-268-8367 (Donna Thomas)
Pittsburgh, PA 15213 address@hidden