[gmx-users] Re: Fluctuations in NVT and NPT resulting plots

Justin Lemkul jalemkul at vt.edu
Sun Oct 21 20:26:30 CEST 2012

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 A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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