I have patched g_order version 4.5.4 to compute the order parameters
in a different way. Despite trying, I don't understand the original
g_order implementation. In the version that I am providing, the
hydrogens are explicitly built and the coordinates of these hydrogens
are output to
Hi Igor,
Thanks for the reply but I think you slightly missed the point I was
trying to make. I followed the approach you mention for the double bond
and (with the two force fields I tried) got the values I discussed in my
last email, which when compared to the published values seem to be
Hi,
Both the trajectories are 100 ns in length (plus I have a repeat of each
simulation using different starting velocities). The results from a
block analysis, and analysis of the repeat simulations, give almost
identical results to those in my previous message. The other thing is
that the
Further to my last message we have managed to use a tcl script in VMD to
calculate the order parameters for the POPC chains in the CHARMM36
simulation. I have put the values for this calculation and the values I
obtained using g_order (over the same period in the same trajectory)
below (this
Dear Thomas:
I agree with your conclusions about g_order.
My usage of the Berger POPC lipids in combination with the g_order
command (as per the instructions in
http://www.gromacs.org/Documentation/Gromacs_Utilities/g_order )
yields order parameters of 0.193 and 0.051 for the first and
chris.ne...@utoronto.ca wrote:
Dear Thomas:
I agree with your conclusions about g_order.
My usage of the Berger POPC lipids in combination with the g_order
command (as per the instructions in
http://www.gromacs.org/Documentation/Gromacs_Utilities/g_order ) yields
order parameters of 0.193
Hi Everyone,
I am facing a problem when calculating the lipid deuterium order
parameters for the unsaturated carbons of the sn-2 tail of POPC using
g_order with GROMACS version 4.5.4 (although I have tried other older
versions too but they all give the same results).
Firstly, I should say
thomas,
i've recently placed a similar question and justin asked me to show my index
for the double bound calculation, so, i'm asking you the same.
you should have
Ci-1
Ci - the first carbon of the double bound
Ci+1 - the second carbon of the double bound
Ci+2
in that index
doing this,
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