Sai Pooja wrote:
Hi,
I have a system of 3600 LJ particles in a plane (using freeze-dimension
option in z). I am running npt runs using Semi-isotropic pressure
coupling with Parrinello-Rahman barostat. I have a few concerns:
1) On the gromacs website, a webpage mentions that this type of pressure
coupling may not be accurate
Please provide a link when making this kind of statement.
2) It takes a really long time for the system to reach the reference
pressure > 500ns. Particularly the Pxx, Pyy terms are very different
and take an extremely long time to converge to a common value.
What was your equilibration protocol? What are your .mdp settings?
-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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