Ángel Piñeiro wrote:
Dear all,
I aim to calculate the lateral diffusion coefficients of lipids as a
function of the distance to a membrane protein using the Martini force
field. For this I guess I could use the diff_mol.xvg output file of the
g_msd command which provides the list of diffusion coefficients for each
lipid (I guess the lipids are ordered as in the trajectory file). Then I
would calculate the protein-lipid distance for each lipid and I would
generate the diffusion vs distance file. Before starting the
calculations on the membrane protein system I tested the g_msd command
on a DPPC bilayer. In my bilayer simulation I removed the COM of lipids
and water separately. Before analyzing it I removed jumps over the box
boundaries using trjconv -pbc nojump and I created a index file with the
PO4 atoms as a new group. Then I executed the following command:
g_msd -s topol.tpr -f trajnojump.xtc -n p.ndx -lateral z -rmcomm
from which I get the following output:
D[ PO4] 0.0958 (+/- 0.0135) 1e-5 cm^2/s
I think the value is not crazy for DPPC at 323 K using Martini... but I
noticed that the D values for the independent lipids reported in the
diff_mol.xvg file range from 0.0021959 to 0.482909 cm^2/s. If the
differences are so high for a single lipid bilayer I suspect that I will
not observe significant differences as a function of the distance to the
protein in my simulations of the whole system... probably I am doing
something wrong¿?
In my experience, this is to be expected. To calculate reliable diffusion
coefficients, you need very well-converged data, and for individual lipids, this
effect is even more pronounced. How long is your trajectory, and how often did
you save snapshots?
Note too, that the results of g_msd can be impacted by -trestart, -beginfit,
-endfit, etc.
-Justin
Thanks for any advice
Ángel Piñeiro.
--
========================================
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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