[gmx-users] Simulation of membrane protein

James Starlight jmsstarlight at gmail.com
Mon Oct 17 09:44:37 CEST 2011


Sure, you could do all of it within a shell script that loops the commands
> and checks the printed output.

As I understood in that iterations only step with scalling by factor 0.95
and futher energy minimization must be included until desired S per lipid
will be reached. Could you provide me with a small example of such script
for better understanding of the syntax. I've never done unix's shell scripts
before :)

Could you tell me where I could found experimental valuee for Area per lipid
for differen cases (e.g I'll be work with large membrane proteins such as
membrane receptors so i wounder to know what values of S per lipid as well
as S per protein I might expect in that case)

Also I have a question about solvation of my membrane protein via GENBOX. I
found 2 possible ways to exclude water from the insertion into membrane
- Changing vdv radii for the C atoms- So i've copied  vdwradii.dat to my
work dirrectory and changed vdv R. How I should to define that genbox uses
exactly that modified file located in my working directory instead of
default vdwradii.dat? Finally how I can check that there are not waters
within the membrane ? (I've tried to visualize via VMD but the overal
picture is very unclear :) )

- Also I've found that I can Running short md to exclude those waters via
hyfrophobic effect.  What parametries would be opti,al for that simulation
in case of KALP as well as other more larger proteins ?

Thank you for your help,

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