Thank Justin so much ! Sorry about my stupid question. I have looked the algorithm and i got it.
On Tue, Jan 22, 2013 at 8:05 PM, Justin Lemkul <[email protected]> wrote: > > > On 1/22/13 12:00 AM, Kieu Thu Nguyen wrote: > >> Thank Justin ! And i used GridMAT-MD as you advised. >> >> I got result "The average bilayer "thickness" will be printed to >> 50x50_average_pbc.dat". But that result is only equal to a half of >> experiment result. I think "bilayer thickness" is equal to the sum of "top >> leaflet thickness" and "bottom leaflet thickness". So should i double "The >> average bilayer "thickness"..." mentioned above ? >> >> > No. The program measures the total thickness, using the reference atoms > you provide. The individual files ("top thickness" and "bottom thickness") > represent two ways of measuring the same thing, using both leaflets as > reference, which are then averaged to produce the desired distance file. > Please refer to our paper for the algorithm. > > > And i do not get average area per lipd, just "The average area per lipid >> in >> the top leaflet is 64.2329395973154 sq. Angstroms. The average area per >> lipid in the bottom leaflet is 63.3821721854305 sq. Angstroms". >> >> > The data file contains areas for each individual lipid, which can be > averaged. > > -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 [email protected] > 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 [email protected]. > * Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
