[gmx-users] order parameter

[Justin A. Lemkul]

Parthasarathi, Ramya wrote:
> 
> 
> 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.
> 

I can't see any image.  Please heed the instructions I provided earlier for 
proper sharing of images.  Embedding usually doesn't work for many mail clients, 
especially those of us who get plain text.

-Justin

> 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
> Ramya
> 
> 
> 
> ________________________________________
> 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
> 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.
> 
> Chris.
> 
> -- original message --
> 
> 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?
> 
> Ramya
> ________________________________________
> 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: 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.
> 
> 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

========================================