[gmx-users] order parameter

Parthasarathi, Ramya ramyasarati at ou.edu
Thu Sep 1 21:29:14 CEST 2011


Hi Justin,

Thanks for the reply, and this is the graph, the red curve is what GROMACS gives, the blue curve is what I get.. yes I am considering the unsaturated carbons in to account. I have to see which is closer to the experimental result.

Hi Chris,

Thanks for the information , I will surely try the VMD tcl script and compute the order parameters and compare.

If there is anything else that you suggest kindly let me know , it will be very helpful for me.

Thanks again

There are several additional points to consider.

1. What type of differences are you getting?  An image would be nice to see,
otherwise no one has any chance of knowing what's going on.  See point number 4


2. Which results are more accurate with respect to experimental results, yours
or those produced by g_order?

3. Are you analyzing saturated or unsaturated chains?  There is a known problem
with g_order's ability to calculated order parameters for unsaturated carbons,
although I'm not sure if it's been filed on redmine yet.  It's been discussed a
number of times.

From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] on behalf of chris.neale at utoronto.ca [chris.neale at utoronto.ca]
Sent: Thursday, September 01, 2011 1:35 PM
To: gmx-users at gromacs.org
Subject: [gmx-users] order parameter

In addition to Justin's comment about g_order being incorrect for
unsaturated carbons, you won't ever get numerical agreement with
g_order, even for saturated carbons, because g_order does not use your
explicit hydrogens. g_order uses the positions of the carbons to
rebuild the hydrogen positions assuming perfect tetrahedral geometry,
which you certainly don't have in all cases when you use real hydrogens.

There is a VMD tcl script that you can download that will compute
order parameters from real hydrogen atoms. perhaps you should try to
compare to that.


-- original message --


Thanks  lot for replying. I am doing all-atom simulation. I am doing
the PBC before finding the angle. also I normalise the vectors before
finding the angle.

Yes I have checked that the formula I am using for the order parameter
is correct.
I am doing the averaging correctly.

1. I take the carbons in each tail ( I neglect the 1st and the last as
GROMACS does) , then I find the Hydrogens associated with it.

2. Then I do the PBC , normalise them and then take the angle, then
calculate the order parameter.

3. finally I average them over the frames.

I have gone through the procedure and still I am not getting the same
profile as GROMACS gives.

Is there anything else that I need to include in my calculations?

From: gmx-users-bounces at gromacs.org [gmx-users-bounces at
gromacs.org] on behalf of chris.neale at utoronto.ca [chris.neale at
Sent: Wednesday, August 31, 2011 8:00 PM
To: gmx-users at gromacs.org
Subject: [gmx-users] order parameter

Dear Ramya:

Are you simulating all-atom lipids (with explicit hydrogen atoms on
the acyl chain)? If not, then you missed a step in your description of
what you have done (g_order, for example, ignores explicit hydrogen
atoms so that it can act on united atom lipids).

Not sure why PBC would be your step #3, after your step #2 was to find
the angle. I suggest that you simply run trjconv -pbc mol on your
trajectory file before you process it and then you no longer need to
worry about PBC in your custom analysis tool.

Once you have the angle, you must average it correctly. The equation
is available in most papers that describe order parameters and is
listed as a comment at the top of the gmx_order.c source file (in
version 4.0.7 at least).

If you want to get more help on your procedure after you have worked
on this for a while, I suggest laying out your procedure very
specifically. Your previous post, for example, was pretty loose with
terminology when you described your method and there is quite a bit
that one must assume.


-- original message --


I am trying to write a code for Deuterium order parameter of DOPC
lipid. I went through the code in gmx_order.c, I did the following,

1.       I took the carbons in the chain, and found its neighbors.
2.       Took the bilayer normal and found the angle between the
bilayer normal and the ?CH molecular axis.
3.       Took care of the periodic boundary conditions since I use NPT

But the code in gmx_order.c in GROMACS tries to do a lot of things
other than this, as I don?t know C or C++ language that it is using, I
don?t know what else I am supposed to include.

Can someone please help me?



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