Parthasarathi, Ramya wrote:
Hi,
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?
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
here:
http://www.gromacs.org/Support/Mailing_Lists#Mailing_List_Etiquette
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.
-Justin
Ramya
________________________________________
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf
of chris.ne...@utoronto.ca [chris.ne...@utoronto.ca]
Sent: Wednesday, August 31, 2011 8:00 PM
To: gmx-users@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.
Chris.
-- original message --
Hi,
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
ensemble.
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?
Ramya
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--
========================================
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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