On 2010-07-15 16.01, Justin A. Lemkul wrote:
Sai Pooja wrote:
Hi,
I am aware there have been many threads on this topic and I have
looked at some of them. I would still like to make this query. I am
running an npt equilibration run for a solvated protein using
Charmm27-Tip3p (nocmap). I ran the simulation for 1ns. The average
values of pressure converge to 1.1 (ref=1.0), however, the
fluctuations are not only large but range from -10^2 --- +10^2. I am
pasting an excerpt from my log file here:
Seems perfectly normal to me.
http://www.gromacs.org/Documentation/Terminology/Pressure#Fluctuation
<snip>
Moreover, in this particular version of gromacs (git version, 20th
June, 2010), RMS fluctuations are not reported in the log file.
mdrun -nocompact
This might be nice to restore, but you can still get all of that from
g_energy.
-Justin
Pooja
--
Quaerendo Invenietis-Seek and you shall discover.
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
[email protected] http://folding.bmc.uu.se
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