James Starlight wrote:
Justin,
2011/10/19 Justin A. Lemkul <jalem...@vt.edu <mailto:jalem...@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
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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