Denny Frost wrote:
from -1000 to 1000, depending on the system. The simulation box is
8x8x8 nm (roughly) and contains about 12,000 atoms
Are the systems even stable? Is there a trend in the pressure, or is it stable
at those values? It seems that the systems are either exploding or imploding.
How long are the simulations? Can you post a complete .mdp file?
-Justin
On Thu, Jan 20, 2011 at 3:09 PM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
Denny Frost wrote:
I am running a variety of NPT simulations with polar, non-polar,
and ionic compounds. Although my results for density agree well
with experimental values, the pressures I get from g_energy are
off by 1 to 3 orders of magnitude. In the log file, the
pressure fluctuates around a lot from -400 to 400 bar, which
seems to be normal according to other posts on this list, but
the average (which is what g_energy gives me) is not 1.0 bar, as
I specified. Does anyone know how to correct this problem?
What is the average value you're getting? How long are your
simulations?
-Justin
Pressure coupling parameters:
Pcoupl = berendsen
pcoupltype = isotropic
tau_p = 1.0
ref_p = 1.0
compressibility = 4.5e-5
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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