[gmx-users] order parameter

[Justin A. Lemkul]

Parthasarathi, Ramya wrote:
> I am sorry I pasted the picture do not know whether it got posted or not so I am attching the figure in JPEG format.
> 

Your code is producing completely unreasonable values, so I would suspect some 
error in whatever you've done.  In this case, Gromacs is providing a very 
reasonable outcome.

-Justin

> Ramya
> ________________________________________
> From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] on behalf of Justin A. Lemkul [jalemkul at vt.edu]
> Sent: Thursday, September 01, 2011 2:31 PM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] order parameter
> 
> 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
>>
>>
>> --
>>
>>
>> --
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
> 
> --
> ========================================
> 
> 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
> 
> ========================================
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> 
> 
> ------------------------------------------------------------------------
> 

-- 
========================================

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

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