[gmx-users] Simulation of membrane protein

Justin A. Lemkul jalemkul at vt.edu
Thu Oct 20 13:36:26 CEST 2011

James Starlight wrote:
> Justin,
> 2011/10/19 Justin A. Lemkul <jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
>     It won't cause errors, per se, but it does indicate that your system
>     is not equilibrated (nor should you expect it to be after only 1
>     ns).  After 20 ns or so of equilibration, most membrane systems
>     should be devoid of internal water and should be well-equilibrated.
> It's crear now. At the current stage I've being tried 20ns equilibration 
> of my same system prepared by G_membed so I hope that I'll get better 
> results in this case :)
>     You'll never get a good comparison.
> I've tried to analysy my system via your GridMAt software  as well as by 
> the GROMACSs functions.
> First of all my system was very stable- the RMSD deviation < 1A and 
> small Rg indicate on the stability of the protein within the membrane as 
> well.
> Also I've obtain S per lipid by GridMat of 68 A^2 that is good result. 
> Finally, I've analyzed Lateral Diffusion of Lipids- this value vas up to 
> 0.1 nm during 1ns stimulation as well as density for lipids groups ( 
> this was near 200 kg m^-3 for both groups ). What values for two last 
> measurements are normal for such system as KALP in DPPC?

Please search the literature.  I don't know what these values should be offhand. 
  I don't know if anyone has made such measurements.

> Finally I wounder to simulate pure lipid bi layer with different force 
> fields ( e.g I want to test Charmm ff). Could I use the md parametries 
> from the KALP simulation for the pure bi-layer ? What are main 
> differences beetween simulation of the pure bilayer and system with the 
> protein?

Different force fields require different settings, most notably cutoffs. 
Understanding the intrinsics of the chosen force field is a prerequisite for 
using it.  Again, time spent in the literature here is more valuable than me 
spitting out settings that you should use.  You'll learn far more by discovering 
it yourself.



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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