VMD-L Mailing List

From: Sebastian Stolzenberg (s.stolzenberg_at_gmail.com)
Date: Sat Nov 07 2009 - 16:48:29 CST

Dear All,

To follow up on the thread below, we quickly debugged the
"orderparam-c2" procedure as part of the "orderparam2.tcl" script posted
below.

The attached, updated "calc_op.tcl"
merely has an additional line:

if { ($i == 9) || ($i == 10) } {

to make sure the first 4 indices do not produce wrong order parameter
values.

Please share any feedback,

George and Sebastian

From: Justin Gullingsrud (justinrocks_at_gmail.com)
Date: Fri Sep 23 2005 - 11:13:16 CDT

Thanks - you're right; I generally used just the c3 routine and hadn't
tested the c2 as thoroughly.

Justin

On 9/23/05, Saladino, Alex <saladinoac_at_upmc.edu> wrote:
> Justin,
> Thanks for the script. I think that you had a couple of errors
involving HT and H1 not being updated and such. I used your loops from
HX HY and added them for HT and H1.
>
> I am sending you the code. Let me know if you agree.
> Alex
>
> -----Original Message-----
> From: Justin Gullingsrud [mailto:justinrocks_at_gmail.com]
> Sent: Wed 9/21/2005 1:26 PM
> To: Nicolas Sapay
> Cc: Saladino, Alex; vmd-l_at_ks.uiuc.edu
> Subject: Re: vmd-l: Lipid Order Parameter
>
>
>
> And of course I forgot to attached the script...
>
>
> On 9/21/05, Justin Gullingsrud <justinrocks_at_gmail.com> wrote:
> > 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"
> >
>
>
> --
> 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"
>
>
>
> 

--
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"