[gmx-users] Simulation of membrane protein

James Starlight jmsstarlight at gmail.com
Thu Oct 20 09:53:46 CEST 2011


2011/10/19 Justin A. Lemkul <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?

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?

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