Intramolecular distances with g_dist

[Martin Hoefling]

Hey Folks,

Problem:
g_dist reads PBC information from the tpr. To calculate intramolecular  
distances, whole molecules and masses from tpr but no PBC treatment  
would be nice.

So far, my workaround is to preprocess trajectories and increase the  
box size with trjconv. Any objections against a small patch  
introducing a -nopbc or -intra switch? If not I would submit it to  
gerrit for the 4.6 release.

Best

Martin

--
Martin Hoefling
Max Planck Institute for Biophysical Chemistry
Theoretical & Computational Biophysics
Am Fassberg 11
37077 Goettingen
Germany
Phone: [phone]
Fax: [phone]
Mail: [hidden email]

[Berk Hess-4]

Hi,

A -intra switch sounds reasonable.

g_mindist doesn't by coincidence already do what you want?

Cheers,

Berk

On 01/20/2012 06:02 PM, Martin Hoefling wrote:

> Hey Folks,
>
> Problem:
> g_dist reads PBC information from the tpr. To calculate intramolecular
> distances, whole molecules and masses from tpr but no PBC treatment
> would be nice.
>
> So far, my workaround is to preprocess trajectories and increase the
> box size with trjconv. Any objections against a small patch
> introducing a -nopbc or -intra switch? If not I would submit it to
> gerrit for the 4.6 release.
>
> Best
>
> Martin
>

[Martin Hoefling]

Am 20.01.2012 18:24, schrieb Berk Hess:

> g_mindist doesn't by coincidence already do what you want?
Well, I need the CoM distance and not the minimum distance. Looking at
g_mindist it interestingly has two options, pi and pbc. I would omit the
pi option so far, since that requires some more work.

Best

Martin