[gmx-users] Thickness

Justin A. Lemkul jalemkul at vt.edu
Tue Mar 16 12:03:31 CET 2010

afsaneh maleki wrote:
> Hi,
> I used bilayer that consisted of 128 DOPC lipids as DOPC128.pdb as the 
> primary bilayer and insert protein in bilayer  with Inflategro program. 
> when i expanded  the bilayer, two DOPC molecules  exited from box. i 
> simulated this system and obtained the thickness of bilayer with 
> GrigMAT_MD. i want to subtract the thickness of pure bilayer from the 
> bilayer that contain the protein.
> would one please elaborate step by step how to subtract the thickness of 
> the pure bilayer( 128 DOPC) from the bilayer (126 DOPC) that contains 
> the protein to get two-dimensional maps of ∆Z that indicate deviation 
> from the thickness of pure bilayer ?

Simply subtract the distances from the output of GridMAT-MD.  The output is just 
a raw matrix of distances at each grid point, so write a script that will run 
through the output and subtract whatever is the appropriate thickness value from 
those numbers.


> Thanks in advance,
> Afsaneh


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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