[gmx-users] density profile

[Elisabeth]

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?

Thanks!

On 31 March 2013 12:21, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 3/31/13 11:41 AM, Elisabeth wrote:
>
>> Dear all,
>>
>> In order to get density profile of a pure system the box has to get
>> extended in one drection (e.g Z) as we do for surface tension calculations
>> or density profile
>> can be also obtained from the usual box filled up with the molecules
>> without need for empty space in Z
>>
>> Thanks for any comments and advise in advance :)
>>
>
> The density of the system is written to the .edr file.  There is no need
> (or use) for a density profile if the system is homogeneous.
>
> -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
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