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:
> 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
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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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