[gmx-users] g_rotacf

Rama Gullapalli quantrum75 at yahoo.com
Mon Sep 25 15:42:59 CEST 2006

Dear Dr Spoel
Thank you for the reply. But I do not quite follow how -noaver does it. 

I want to compute the P-N vector of lipid molecules and average  it over the 128 molecules in the bilayer.

Do I make a group containing the numbers of the P and N molecules in a single group ( 256 atoms) and use g_rotacf with -noaver?
Will that compute the rotational correlation of the individual P-N vectors of each lipid molecule and average it over 128 molecules?

Thanks in advance

David van der Spoel <spoel at xray.bmc.uu.se> wrote: On Fri, 22 Sep 2006, Rama Gullapalli wrote:

>Hello everybody,
>  I have nearly 100 different vectors to analyse using g_rotacf. I was  wondering if there was anyway to do this in GROMACS simultaneously  since g_rotacf does not have have the -ng option like in g_traj or  others.


>  I would imagine one could use a awk script to run g_rotacf to run a  hundred times, but I am not sure how to go about it. If anyone can  provide me with pointers on that it would be great
>  Thanks in advance
>  Rama
>Talk is cheap. Use Yahoo! Messenger to make PC-to-Phone calls.  Great rates starting at 1¢/min.

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,   75124 Uppsala, Sweden
phone: 46 18 471 4205  fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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