VMD-L Mailing List

From: Justin Gullingsrud (justinrocks_at_gmail.com)
Date: Wed Sep 21 2005 - 12:26:12 CDT

Here's a script I've used to calculate lipid order parameters. It
averages over all frames in your molecule, which is usually what you
want. Usage is like so:

# Store order parameter data in array named arr
orderparam-c3 arr

# Store order parameter data for just the top monolayer
orderparam-c3 arr {same residue as "name P.*" and z > 0}

# Write out data to a file
set fd [open mydata.dat w]
foreach key [lsort -integer [array names all]] {
  puts $fd [list $key $arr($key)]
}
close $fd

Cheers,
Justin

On 21 Sep 2005 09:44:45 +0200, Nicolas Sapay <n.sapay_at_ibcp.fr> wrote:
> Alex,
> I have made a Python script that compute |Scd|, but it works with the
> MDTools python module
> (http://www.ks.uiuc.edu/Development/MDTools/Python/), not with VMD.
> However, the script is commented. So, I think it would be not too much
> difficult to adapt it to VMD. Contact me if you are interested.
>
> Nicolas
>
> Le mar 20/09/2005 à 23:21, Saladino, Alex a écrit :
> > Does any one have a script to calculate the order parameter for a lipid molecule?
> >
> > Thank you,
> > Alex
> --
> _ Nicolas Sapay ____________________________________________
> Ph.D sudent in structural bioinformatics
> Institut de Biologie et Chimie des Proteines
> CNRS - Claude Bernard University, IFR128 Bioscience Lyon-Gerland
> 7, Passage du Vercors Tel: +33 (0)4 72 72 26 46
> 69367-F Lyon cedex 07 Fax: +33 (0)4 72 72 26 04
> France Web: http://pbil.ibcp.fr/
>
>
> 

--
The spirit of Plato dies hard.  We have been unable to escape the
philosophical tradition that what we can see and measure in the world
is merely the superficial and imperfect representation of an
underlying reality.
                -- S.J. Gould, "The Mismeasure of Man"