[gmx-users] Re: ED analysis

[Anton Feenstra]

vincenzo venditti wrote:

> Dear Anton,
> in a previous mail about combined ED analysis of MD trajectories, you have said 
> you have averaged together more 1ns MD trajectories. How can I do this with 
> GROMACS tools?

I'm not sure what you mean with 'averaged'.

As for the ED analysis, it is very simple. You cat together all the 
trajectories you want to analyze together, like:

cat run1.xtc run2.xtc run3.xtc > all.xtc

Then you can do the covariance calculation, like:

g_covar -s topol.tpr -f all.xtc

and, finally, you can project all trajectories, or separate ones, using 
g_anaeig like you would do for a normal ED analysis.

P.S., please refer these questions simply through the list. I'll answer 
as well (when I can find the time) but someone else may answer sooner 
and/or better! (and, it'll be archived)


-- 
Groetjes,

Anton

* NOTE: New Phone & Fax numbers (below) *

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|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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