[gmx-users] density profile

[Justin Lemkul]

On 3/31/13 12:27 PM, Elisabeth wrote:
> Thank Justin. I am interested in the density profile at the solvent-air
> interface. I wanted to see how density changes with position at different
> pressures...I have the equilibrated boxes at several pressures obtained
> from NPT but I am not sure whether running g_density on the current
> simulations cells provides the profile I am after. Do you have any clue
> whether or not the cell has to be extended in one direction to obtain the
> density profile?
>

If you're trying to produce an air-water interface, then indeed you will need 
some model for air within the unit cell, but there are several practical 
problems with that.  The first is that g_density does not deal well with 
changing box vectors, and the density profiles it produces under an NPT ensemble 
are incorrect (outstanding bug that needs to be fixed, IIRC).  The second is 
that if you run a simulation under NPT with void space, the unit cell will just 
compress down until there is no empty space.  Probably the best solution would 
be to equilibrate under NPT at the desired conditions, then build a new unit 
cell and run under NVT.  Using NVT will circumvent both problems, and if the 
proper pressure, density, etc have already been achieved, then you've got what 
you're after.

-Justin

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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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