Hi Justin, On Thu, Jan 18, 2018 at 5:42 AM, Justin Lemkul <jalem...@vt.edu> wrote:
> > > On 1/18/18 12:24 AM, Mohsen Ramezanpour wrote: > >> Dear Gromacs users, >> >> I am interested in calculation of tilt angle for the POPC headgroup (angle >> distribution between the P-N vector and Z axis). >> I am not sure if my approach is correct as my angle distribution does not >> seem reasonable. >> >> Given a bilayer with 200 lipids (100 lipids in each leaflet with >> resides 1-100 and 101-200 for upper and lower leaflets, respectively) >> simulated for 200 ns: >> >> gmx make_ndx -f SYSTEM.gro -o index.ndx >> keep 0 >> r 1-100 >> name 1 upperleaflet >> 1 & a P >> 1 & a N >> 2 | 3 >> name 4 vector >> q >> >> Next, I use: >> gmx gangle -f md.xtc -s md.tpr -n index.ndx -g1 vector -g2 z >> -b >> 100000 -group1 -oh histogram.xvg -binw 0.01 >> >> and choose index group 4 and then Ctrl+D. >> >> Please let me know your opinion. I think I am doing something wrong, >> especially with the construction of P-N vector. >> > > What results do you get from this approach? > A normal distribution centered around 105 with a high pick standing out around 90. I expected it to be around ~73-77 > > What happens if you try to analyze only a single lipid? > I get an approximate normal distribution centered around 100 degrees. I have two systems, one is salt free and the other one has 0.15 M NaCL salt. The shape of histograms is the same. I had to separate the leaflets, right? So, any idea why this is happening? > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Virginia Tech Department of Biochemistry > > 303 Engel Hall > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.biochem.vt.edu/people/faculty/JustinLemkul.html > > ================================================== > > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/Support > /Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- *Rewards work better than punishment ...* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.