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<br>
Hi Justin,<br>
<br>
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.
<br>
<br>
Hi Chris,<br>
<br>
Thanks for the information , I will surely try the VMD tcl script and compute the order parameters and compare.<br>
<br>
If there is anything else that you suggest kindly let me know , it will be very helpful for me.<br>
<br>
Thanks again<br>
Ramya<br>
<br>
<br>
<br>
________________________________________<br>
<font size="2"><span style="font-size: 10pt;">There are several additional points to consider.<br>
<br>
1. What type of differences are you getting? An image would be nice to see, <br>
otherwise no one has any chance of knowing what's going on. See point number 4 <br>
here:<br>
<br>
<a href="http://www.gromacs.org/Support/Mailing_Lists#Mailing_List_Etiquette" target="_blank">http://www.gromacs.org/Support/Mailing_Lists#Mailing_List_Etiquette</a><br>
<br>
2. Which results are more accurate with respect to experimental results, yours <br>
or those produced by g_order?<br>
<br>
3. Are you analyzing saturated or unsaturated chains? There is a known problem <br>
with g_order's ability to calculated order parameters for unsaturated carbons, <br>
although I'm not sure if it's been filed on redmine yet. It's been discussed a <br>
number of times.<br>
<br>
-Justin</span></font><br>
From: gmx-users-bounces@gromacs.org [gmx-users-bounces@gromacs.org] on behalf of chris.neale@utoronto.ca [chris.neale@utoronto.ca]<br>
Sent: Thursday, September 01, 2011 1:35 PM<br>
To: gmx-users@gromacs.org<br>
Subject: [gmx-users] order parameter<br>
<br>
In addition to Justin's comment about g_order being incorrect for<br>
unsaturated carbons, you won't ever get numerical agreement with<br>
g_order, even for saturated carbons, because g_order does not use your<br>
explicit hydrogens. g_order uses the positions of the carbons to<br>
rebuild the hydrogen positions assuming perfect tetrahedral geometry,<br>
which you certainly don't have in all cases when you use real hydrogens.<br>
<br>
There is a VMD tcl script that you can download that will compute<br>
order parameters from real hydrogen atoms. perhaps you should try to<br>
compare to that.<br>
<br>
Chris.<br>
<br>
-- original message --<br>
<br>
Hi,<br>
<br>
Thanks lot for replying. I am doing all-atom simulation. I am doing<br>
the PBC before finding the angle. also I normalise the vectors before<br>
finding the angle.<br>
<br>
Yes I have checked that the formula I am using for the order parameter<br>
is correct.<br>
I am doing the averaging correctly.<br>
<br>
1. I take the carbons in each tail ( I neglect the 1st and the last as<br>
GROMACS does) , then I find the Hydrogens associated with it.<br>
<br>
2. Then I do the PBC , normalise them and then take the angle, then<br>
calculate the order parameter.<br>
<br>
3. finally I average them over the frames.<br>
<br>
I have gone through the procedure and still I am not getting the same<br>
profile as GROMACS gives.<br>
<br>
Is there anything else that I need to include in my calculations?<br>
<br>
Ramya<br>
________________________________________<br>
From: gmx-users-bounces at gromacs.org [gmx-users-bounces at<br>
gromacs.org] on behalf of chris.neale at utoronto.ca [chris.neale at<br>
utoronto.ca]<br>
Sent: Wednesday, August 31, 2011 8:00 PM<br>
To: gmx-users at gromacs.org<br>
Subject: [gmx-users] order parameter<br>
<br>
Dear Ramya:<br>
<br>
Are you simulating all-atom lipids (with explicit hydrogen atoms on<br>
the acyl chain)? If not, then you missed a step in your description of<br>
what you have done (g_order, for example, ignores explicit hydrogen<br>
atoms so that it can act on united atom lipids).<br>
<br>
Not sure why PBC would be your step #3, after your step #2 was to find<br>
the angle. I suggest that you simply run trjconv -pbc mol on your<br>
trajectory file before you process it and then you no longer need to<br>
worry about PBC in your custom analysis tool.<br>
<br>
Once you have the angle, you must average it correctly. The equation<br>
is available in most papers that describe order parameters and is<br>
listed as a comment at the top of the gmx_order.c source file (in<br>
version 4.0.7 at least).<br>
<br>
If you want to get more help on your procedure after you have worked<br>
on this for a while, I suggest laying out your procedure very<br>
specifically. Your previous post, for example, was pretty loose with<br>
terminology when you described your method and there is quite a bit<br>
that one must assume.<br>
<br>
Chris.<br>
<br>
-- original message --<br>
<br>
Hi,<br>
<br>
I am trying to write a code for Deuterium order parameter of DOPC<br>
lipid. I went through the code in gmx_order.c, I did the following,<br>
<br>
1. I took the carbons in the chain, and found its neighbors.<br>
2. Took the bilayer normal and found the angle between the<br>
bilayer normal and the ?CH molecular axis.<br>
3. Took care of the periodic boundary conditions since I use NPT<br>
ensemble.<br>
<br>
But the code in gmx_order.c in GROMACS tries to do a lot of things<br>
other than this, as I don?t know C or C++ language that it is using, I<br>
don?t know what else I am supposed to include.<br>
<br>
Can someone please help me?<br>
<br>
Ramya<br>
<br>
<br>
--<br>
<br>
<br>
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