On Fri, Jan 19, 2018 at 5:55 AM, Justin Lemkul <jalem...@vt.edu> wrote:
> > > On 1/18/18 1:28 PM, Mohsen Ramezanpour wrote: > >> 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 >> > > Upon what are you basing your expectation? Previous literature? Some other > calculation or visual inspection? It is mentioned upon the last paragraph of left column at page (3777) in this article: Saches et al. Biophys J <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1304278/#>. 2004 Jun; 86(6): 3772–3782 > > >> 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? >> > > If the membrane is homogeneous, I don't see any reason why. Choosing z axis to calculate the angle distribution for, P->N vector has opposite directions (in average) between two leaflets. for one leaflet one makes (Just as an example) a normal distribution centered around 73, and the lower leaflet will make a normal distribution centered around (180-73). However, if we consider both, we will get a normal distribution centered around ~90. This is why I think we must separate those, even for a homogenous bilayer. Is this reasonable? > > > -Justin > > > 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. >>> >>> >> >> > -- > ================================================== > > 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.