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 stdout
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
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 sec
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 is
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 r
Thomas Piggot wrote:
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 publishe
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
inc
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 t
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 th
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