[gmx-users] Measure of density in homo- and heterogeneous systems
jmsstarlight at gmail.com
Tue May 29 07:21:23 CEST 2012
the main problem is the my simulation in nvt ensemble :) I understand that
density is constant in that conditions but I'd like to find way to check
this values for different components of my system.
2012/5/28 Justin A. Lemkul <jalemkul at vt.edu>
> On 5/28/12 3:09 PM, James Starlight wrote:
>> Dear Gromacs users!
>> In this task I have two systems:
>> First system consist of single layer of Ccl4 molecules.
>> Second system consist of membrane-mimicking layer of Ccl4 surrounded by
>> and the protein embedded in that biphastic layer.
>> I'd like to measure density in both of my systems to check of its packing
>> degree. How could I do it in the case of homo system- (where I'd like to
>> density in the Ccl4 layer only) as well as in more complex hetero system
>> where I'd like to check density in each layer separately as well as
>> averaged density among all layers) ?
> The density of the homogeneous system can easily be obtained from the .edr
> file, as long as the ensemble was NPT. With NVT, the density term is not
> written, IIRC.
> In the case of the heterogeneous system, use g_density to obtain partial
> densities as a function of box dimension.
> 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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