[gmx-users] Measure of density in homo- and heterogeneous systems

[James Starlight]

Justin,

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.


James

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
>> water
>> 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
>> check
>> 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
>> compute
>> 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
>
> --
> ==============================**==========
>
> 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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================**==========
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
> Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
> Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20120529/850d5f0a/attachment.html>