[gmx-users] Fwd: how to calculate angles (molecules directions)

[Maryam Kowsar]

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.neale at 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-bounces at maillist.sys.kth.se <
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Maryam
> Kowsar <maryam.kowsar at gmail.com>
> Sent: 13 February 2015 00:19
> To: gmx-users at 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.neale at 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-bounces at maillist.sys.kth.se <
> > gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Maryam
> > Kowsar <maryam.kowsar at gmail.com>
> > Sent: 12 February 2015 23:59
> > To: gmx-users at 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.neale at 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-bounces at maillist.sys.kth.se <
> > > gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Maryam
> > > Kowsar <maryam.kowsar at gmail.com>
> > > Sent: 12 February 2015 23:45
> > > To: gromacs.org_gmx-users at maillist.sys.kth.se
> > > Subject: [gmx-users] Fwd: how to calculate angles (molecules
> directions)
> > >
> > > ---------- Forwarded message ----------
> > > From: Maryam Kowsar <maryam.kowsar at gmail.com>
> > > Date: Fri, Feb 13, 2015 at 12:14 AM
> > > Subject: how to calculate angles (molecules directions)
> > > To: gromacs.org_gmx-users at 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
> > > --
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