[gmx-users] Regarding g_sgangle index file

Venkat Reddy venkat4bt at gmail.com
Tue Sep 24 07:39:20 CEST 2013

Hello Sir,
I have been using the new tool "gmx gangle". My actual intention is to
calculate the orientation between any two same molecules (say cholesterol)
throughout the trajectory and there are 40 cholesterol molecules. But I
couldn't calculate it. I am getting "0" as output. My command is:
gmx gangle -f traj_noPBC.xtc -s topol.tpr -n -g1 vector -g2 vector -group1
'resname CHOL and name R5 R0' -group2 'resname CHOL and name R5 R0' -oav
-oall -oh

On Mon, Sep 23, 2013 at 11:19 PM, Teemu Murtola <teemu.murtola at gmail.com>wrote:

> Hi,
> On Thu, Sep 19, 2013 at 7:19 PM, Venkat Reddy <venkat4bt at gmail.com> wrote:
> > @Teemu Murtola: Are there any modifications to the other gmx tools? (eg:
> > rdf calculation with dynamic selection...etc). I am trying to explore the
> > new version.
> >
> Unfortunately, there are currently very few tools using the new mechanisms.
> http://www.gromacs.org/Documentation/How-tos/Tool_Changes_for_5.0 lists
> most of the changes: in practice, there's 'gmx distance' as a more flexible
> alternative to computing distances, and g_select (now 'gmx select') has
> gotten a few extra output options. There's also at least one new tool, 'gmx
> freevolume'.
> Best regards,
> Teemu
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With Best Wishes
Venkat Reddy Chirasani
PhD student
Laboratory of Computational Biophysics
Department of Biotechnology
IIT Madras

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