Hi Teemu, Thanks for the reply. Unfortunately, i cannot upgrade to 5.0.6 right now ( i have to ask to the admin of the cluster first, and so on and so far). I do can downgrade to 4.6.3 and use g_dist instead. I have read some papers where people claimed to have been used g_dist to measure the thickness of a bilayer, but I wasn’t capable to do that. I created 3 different groups: All PO4 beads of the bilayer: G1 PO4 beads of the top leaflet of the bilayer: G2 PO4 beads of the bottom leaflet of the bilayer: G3 but considering that g_dist used the COM of the groups when i used g_dist as following: g_dist -f POPC-300K-2us.xtc -s POPC-300K-2us.tpr -n index.ndx -o PO4-distance
If i select group 1 and 2 as group G1 i got a distance of 0 (which i think it make sense, considering that g_dist use the COM of a group) but when i select group 1: G2 and group 2: G3 (PO4 beads of the top and bottom leaflet respectively) i got really nice values: ~3.9 at 300K ~3.8 at 328K with an standard deviation of ~0.002 each (considering the Z component, of course) Are this results ok? Can i use this approximation (measuring the distance between the top and bottom PO4 beads of a bilayer) to get the membrane thickness of a bilayer? Best, Carlos -- Carlos Navarro Retamal Bioinformatics Engineering Ph. D (c) Applied Sciences. Center of Bioinformatics and Molecular Simulations. CBSM University of Talca Av. Lircay S/N, Talca, Chile T: (+56) 712201 798 E: carlos.navarr...@gmail.com or cnava...@utalca.cl On July 28, 2015 at 3:17:47 PM, Teemu Murtola (teemu.murt...@gmail.com<mailto:teemu.murt...@gmail.com>) wrote: Please upgrade to 5.0.6. There was a bug with gmx distance -oxyz that caused the output file to not appear (or to overwrite some unintended files), which was fixed for the latest version. On Tue, Jul 28, 2015, 17:34 Carlos Navarro Retamal <cnava...@utalca.cl> wrote: > Hi Justin, > thanks for your reply. > Is there a way, to analyse each component (x,y,z) of the distance without > the flag -oxyz? > For some reason, I’m unable to get this data with gmx distance. > In fact, when i ran > gmx distance -f trajout329K.xtc -s POPC-329K-2us.tpr -n index.ndx -oxyz > the command line doesn’t generate anything (any *xvg file). > I don’t know what I’m doing wrong > Best, > Carlos > -- > Carlos Navarro Retamal > Bioinformatics Engineering > Ph. D (c) Applied Sciences. > Center of Bioinformatics and Molecular Simulations. CBSM > University of Talca > Av. Lircay S/N, Talca, Chile > T: (+56) 712201 798 > E: carlos.navarr...@gmail.com or cnava...@utalca.cl > > > > On July 28, 2015 at 9:34:32 AM, Justin Lemkul (jalem...@vt.edu<mailto: > jalem...@vt.edu>) wrote: > > July 28, 2015 at 6:09:51 AM GMT-3 ro Retamal wrote: > > Dear gmx users, > > I’m studying the implication of higher temperatures in the membrane > thickness (d) of several bilayer during CGMD simulations. > > In order to measure d in a pure POPC membrane i create an index group > containing only PO4 beads. > > Before everything, i remove PBC conditions in the simulations as > following: > > trjconv -f POPC-300K-2us.xtc -s POPC-300K-2us.tpr -pbc nojump -o > trajout300K.xtc > > trjconv -f POPC-329K-2us.xtc -s POPC-329K-2us.tpr -pbc nojump -o > trajout329K.xtc > > > > Then, I used gmx distance: > > gmx distance -f trajout300K.xtc -s POPC-329K-2us.tpr -n index.ndx -oav > avg-300K > > gmx distance -f trajout329K.xtc -s POPC-329K-2us.tpr -n index.ndx -oav > avg-329K > > > > Finally, using g_analyse i analyse both *xvg files and i got: > > > > 300K: > > Average distance: 4.090 nm > > Standard deviation: 1.451 nm > > > > 329K: > > Average distance: 4.134 nm > > Standard deviation: 1.515 nm > > > > Those are pretty massive standard deviations; I wouldn't expect a membrane > to > fluctuate quite that much. Are you averaging only the z-component of the > distance? > > > Is it normal, that I’m getting a higher thickness at higher temperature? > Or are my results are ‘ok', considering the values of both standard > deviation? > > Your results are indistinguishable, given the huge standard deviations. > > -Justin > > > In any case; I think this is strange, because using a different > approximation/methods (GridMAT-MD) i got at 300K, d= 3.996 and at 329K d= > 3.869 ( more ‘normal’ results for this type of lipid at this temperatures). > > Am i missing something with my approximation that is 'disrupting' my > results? > > I’ll prefer to use gmx distance to analyse d in my simulations, > considering the extensive amount of time that will take me if i use > GridMAT-MD to analyse my 1us of production data. > > Any thoughts/suggestions are more than welcome. > > Best, > > Carlos > > > > > > -- > > Carlos Navarro Retamal > > Bioinformatics Engineering > > Ph. D (c) Applied Sciences. > > Center of Bioinformatics and Molecular Simulations. CBSM > > University of Talca > > Av. Lircay S/N, Talca, Chile > > T: (+56) 712201 798 > > E: carlos.navarr...@gmail.com or cnava...@utalca.cl > > > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > ================================================== > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? 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