In my case for second order parameter I need the angle between the unit vector linking N- and C-termini of the ith peptide and the d (the director) is a unit vector defining the preferred direction of alignment.
These vectors are not clear to me.. please suggest something. Nidhi On Sat, Jun 3, 2017 at 5:10 AM, André Farias de Moura <mo...@ufscar.br> wrote: > Hi Nidhi, > > In short: you are using a general-purpose software, so it does not have > tools for all specific applications any user might be interested in. Either > you have to hack/adapt existing analysis tools or you have to write your > own tools. > > That being said: the director is a rather arbitrary direction even > experimentally, it becomes well-defined only when you have an external > field (usually magnetic or electric, maybe both) or an interface, so the > director would be either the direction of the field or the direction > perpendicular to the interface, respectively. > > Anyway, it is up to you to decide which direction makes sense as the > director of your system. Once you choose that vector and a vector defining > what you are naming "molecular axis", calculating angles and correlation > functions to obtain any sort of order parameter can be accomplished > straightforwardly using any spreadsheet. > > (pretty much the same Antonio had already told you) > > Andre > > On Fri, Jun 2, 2017 at 6:21 PM, nidhi sorout <nidhi020...@gmail.com> > wrote: > > > Hello, > > > > Thank you Antonio.. > > > > But my angle of interest is the angle between the molecular axis of > protein > > and the director. I am not able to understand here, from where I can > choose > > this 'director'? > > > > Nidhi > > > > On 30 May 2017 8:55 p.m., "Antonio Baptista" <bapti...@itqb.unl.pt> > wrote: > > > > > Hi Nidhi, > > > > > > If I remember correctly (and your use of "p2" suggests so), that should > > be > > > the ensemble average of the 2nd-order Legendre polynomial of the angle > > > between the molecular axis and the membrane normal, right? > > > > > > Although the order parameter computed by "gmx order" uses that same > > > definition, it takes each C-H bond of the aliphatic lipid tail, not the > > > overall molecular axis. So, "gmx order" is not what you want. > > > > > > You can in principle compute what you need in two steps: (1) use "gmx > > > gangle" to compute the angle of interest for all molecules and all > > > snapshots (you will have to defined the vector of interest, say as the > > one > > > connecting the tail to the head); (2) do a small script to compute the > > > average from those data. > > > > > > Best, > > > Antonio > > > > > > > > > On Tue, 30 May 2017, nidhi sorout wrote: > > > > > > Dear All, > > >> I want to calculate the nematic order parameter (p2) at each time > step. > > >> Is it possible to do this with "gmx order"? > > >> If not than please suggest the right way. > > >> > > >> Thank you, > > >> Nidhi > > >> -- > > >> 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. > > >> > > >> -- > > > 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. > > > > > -- > > 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. > > > > > > -- > _____________ > > Prof. Dr. André Farias de Moura > Department of Chemistry > Federal University of São Carlos > São Carlos - Brazil > phone: +55-16-3351-8090 > -- > 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. > -- 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.