grivet wrote:
Le lundi 31 mai 2010 à 10:29 -0400, Justin A. Lemkul a écrit :
Justin A. Lemkul wrote:
grivet wrote:
Dear all,
I am running simulations of pure water at various temperatures. My first
step is an annealing from the previous temperature to the next one,
using a NPT ensemble. Using the result of that, I run an NVT simulation.
Where can I recover the box average box dimensions, volume and density
of water in the NVT run ?
Use g_energy.
Appaerently no; g_energy gives me a choice of 37 variables to print
(energies, pressure tensor, virial, etc..) but not box dimensions,
volume or density. Is this because I am using 4.0.5 ?
No, it's probably because you're using an NVT ensemble. See the comment from my
previous message. If the values can't change then they likely won't be written
to the .edr file (since it's a waste of space).
-Justin
I should also add that under an NVT ensemble, none of these values will have
changed from whatever the initial conditions were. Only under the influence of
pressure coupling does the density vary (since the box vectors fluctuate).
Volume is constant by virtue of the fact that you're using NVT.
-Justin
Using g_density, I am surprised to find that the density is varying by
several percent; shouldn't it remain constant ?
Thanks in advance for your insights
JP Grivet
My mistake. g_density outputs *partial* densities, with a default number
of slices = 50. Setting -sl 0 recovers a single normal density.
--
========================================
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
========================================
--
========================================
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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