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 <jalem...@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@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-requ...@gromacs.org. > Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >
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