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

[Christopher Neale]

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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