Dear Christopher, I will try the ways you mentioned. One of them should work! I wanted a faster way than writing a code. However, if nothing works, I have to try programming.at last. Thanks a lot!
Cheers, --Maryam On Fri, Feb 13, 2015 at 8:51 AM, Christopher Neale < chris.ne...@alum.utoronto.ca> wrote: > Sure.. hope it works. If not, then yes g_traj just gives you the > positions, but you know the charges and you can compute the dipole > yourself. I know, not an ideal solution, but I was just mentioning it since > you may be forced to use it. Even better, write your own gromacs analysis > tool by taking a very simple tool and re-purposing it. However, if you > don't know C programming, then g_traj + awk can get you most any analyses > that you need (though slowly). > > Chris. > > ________________________________________ > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Maryam > Kowsar <maryam.kow...@gmail.com> > Sent: 13 February 2015 00:19 > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Fwd: how to calculate angles (molecules > directions) > > Dear Christopher, > > I tried g_traj -ox but it just gives me the positions not the orientations. > I think I should try g_dipole. > thank you very much! > > Cheers, > --Maryam > > > On Fri, Feb 13, 2015 at 8:42 AM, Christopher Neale < > chris.ne...@alum.utoronto.ca> wrote: > > > Dear Maryam: > > > > I don't know. If g_dipoles doesn't give you what you want (and I have no > > idea if it will), then g_traj -ox will give you positions that you can > then > > run a script over to compute things yourself. Probably somebody else can > > offer more advice here. > > > > Chris. > > > > ________________________________________ > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < > > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Maryam > > Kowsar <maryam.kow...@gmail.com> > > Sent: 12 February 2015 23:59 > > To: gmx-us...@gromacs.org > > Subject: Re: [gmx-users] Fwd: how to calculate angles (molecules > > directions) > > > > Hi Christopher, > > > > You are on the right side! I mean the angle between the dipole moment > > vector of a molecule and a special vector (for a very simple assumption X > > axis for example). I found two options g_angle and g_sgangle but I think > > non of them can help. Are there any other commands to use? > > thank you! > > > > On Fri, Feb 13, 2015 at 8:18 AM, Christopher Neale < > > chris.ne...@alum.utoronto.ca> wrote: > > > > > How does one compute the angle between a vector and a molecule? I think > > > you need to define your goal more completely. > > > > > > ________________________________________ > > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < > > > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Maryam > > > Kowsar <maryam.kow...@gmail.com> > > > Sent: 12 February 2015 23:45 > > > To: gromacs.org_gmx-users@maillist.sys.kth.se > > > Subject: [gmx-users] Fwd: how to calculate angles (molecules > directions) > > > > > > ---------- Forwarded message ---------- > > > From: Maryam Kowsar <maryam.kow...@gmail.com> > > > Date: Fri, Feb 13, 2015 at 12:14 AM > > > Subject: how to calculate angles (molecules directions) > > > To: gromacs.org_gmx-users@maillist.sys.kth.se > > > > > > > > > Dear users, > > > Is there a way in GROMACS to calculate the angle of each molecule with > a > > > specified vector in each step? > > > Thank you in advance. > > > Regards, > > > --Maryam > > > -- > > > 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. > > -- > > 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. > -- 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.
