[gmx-users] Re: Re,I have a problem with my biphasic system

Justin Lemkul jalemkul at vt.edu
Fri Nov 2 17:53:06 CET 2012

On 11/2/12 11:48 AM, Ali Alizadeh wrote:
> Dear Justin
> I wanted to check that Did i simulate?
> I said if i multiplied average number density(from each part of
> profile) to volume and summation of them was nearly number of
> my total number of particle, i can say my simulation is correct, I did
> it but result completely conflicted with my total number,(three or
> four time my particles)!
> In your opinion, my idea is correct?

Doing so will tell you nothing about whether your "simulation is correct."  The 
problem is that it is very difficult to measure what you want.  You can get 
partial densities along one dimension with g_density (caveats aside about the 
accuracy of this method), but you need the total volume to take the partial 
densities and convert them to particle numbers.  I know of no way to directly 
measure these, since the partial densities vary as a function of box length.  I 
really don't see much of a point in doing this, because all it verifies is that 
the number of particles is fixed, which you already know to be true.



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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