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

[Christopher Neale]

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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