VMD-L Mailing List

From: Cesar Luis Avila (cavila_at_fbqf.unt.edu.ar)
Date: Wed May 30 2007 - 20:36:09 CDT

I am using the script contributed by justin gullingsrud and revised by
Alex Saladino
http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/5378.html
I think that it considers a planar bilayer.

I have used it over a 10 ns simulation on a medium-sized DMPC membrane
(369 lipids) in interaction with a protein which is not embedded but in
close contact with the top hemilayer. I should say that the script is
very quick (may be less than a minute for 100 frames). The problem I am
facing is that the order parameter, as measured with this script, is
constantly rising over time. Could it be possible that I am having
ondulations on the membrane and as a consequence this script is not
valid anymore?

I would deeply appreciate if you could share your script so I might be
able to contrast the results obtained by both approaches.

The distance between phosphorus from both bilayers is also increasing,
but very slowly.

Regards
Cesar

Axel Kohlmeyer escribió:
> On Wed, 30 May 2007, Richard Swenson wrote:
>
>
> RS> I am new to tcl scripting for VMD, but have written script that computes
> RS> the bilayer normal and corresponding lipid order parameters for each
> RS> lipid in a non-planar bilayer. Unfortunately, the script will take
> RS> about a month to finish. Does anyone have a better script or any tips
> RS> on how to speed up performance?
>
> where is the script?
>
> axel.
>
> RS>
> RS> Thanks for the help!
> RS> Richard
> RS>
>
>