[gmx-users] Z-position calculation

[Sarah Witzke]

Hi,

To get the z coordinate of the center of mass of a molecule I use the following command:

echo "number of molecule"  | g_traj -f xxx.xtc -s xxx.tpr -n xxx.ndx -nox -noy -com -ox xxx.xvg

I guess you can create an .ndx file for a lipid head group to get the z coordinate of this.

Regards,
Sarah


-----Original Message-----
From: gmx-users-bounces at gromacs.org on behalf of TJ Piggot
Sent: Tue 06-10-2009 11:55
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Z-position calculation
 
Hi,

You could also try g_bundle -z, it might do what you want.

Cheers

Tom

--On Tuesday, October 06, 2009 11:04:29 +0200 XAvier Periole 
<x.periole at rug.nl> wrote:

>
>
> g_traj with an index and playing with the different options.
>
>
>
> On Oct 6, 2009, at 11:01 AM, Moutusi Manna wrote:
>
> Dear all,
>              I want to calculate the vertical position (Z-axis) of
> different lipid head groups as a function of time.
>              Looking forward for any suggestion.
>              Thanks in advance,
>  Moutusi Manna
>
>
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----------------------
TJ Piggot
t.piggot at bristol.ac.uk
University of Bristol, UK.

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