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.
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.
--
========================================
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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