On 10/21/12 2:11 PM, Ali Alizadeh wrote:
Dear Justin
As you said, fluctuation of v is normal in npt ensemble, How can i
represent my density result(i take samples in each frame)?
In your opinion are my results reliable? Total number of my molecules
is constant all of the simulation time,
volume is changing. Will i get logical number density profile?
Is this related to the previous thread regarding your issues with a
heterogeneous symmetrical system? If it is, please do not start a new thread;
continue the old one. I'm not going to re-discuss things that have already come
up and I think Chris gave you a wealth of information already.
g_density may have problems with systems under NPT, that's a given. If you have
a homogeneous system, then the density is stored in the .edr file.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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