[gmx-users] Order parameters of lipid

Alan Dodd anoddlad at yahoo.com
Fri Aug 1 13:00:56 CEST 2008 

Yes, I never managed to get a later version of g_order to function properly.  I only ever get the -Sg and -Sk outputs, no matter WHAT I put in the index files.  I've just kept an old version of gromacs on the machine I use for analysis.  A copy of 3.2.1 should be quite easy to download, and will definitely work using the approach you've been told.  I'm pretty sure that if you get it wrong, you just end up with empty output, so if you get numbers then you're doing it right.
Incidentally, I always get a sawtooth-shaped curve from my g_order.  Anyone know if this is something simple, like a sampling issue, or indicative of something more serious?  I'm fairly sure I've seen it in published MD work with bilayers, but that doesn't mean it's right of course.



----- Original Message ----
From: Justin A. Lemkul <jalemkul at vt.edu>
To: Gromacs Users' List <gmx-users at gromacs.org>
Sent: Friday, August 1, 2008 11:19:33 AM
Subject: Re: [gmx-users] Order parameters of lipid



minnale wrote:
>  
> 
> Thanks to Justin for his suggestion
> I tried the way mentioned in http://wiki.gromacs.org/index.php/make_ndx. 
> I made index file with seperate groups and feed to g_order command
> g_order -f .xtc -s .tpr -od scd.xvg -o ord -n .ndx
> Group    0 (        C34) has  128 elements
> Group    1 (        C36) has  128 elements
> Group    2 (        C37) has  128 elements
> .
> .
> .
> .
> .
> .
> . and so on till Group    15 (        C50) has  128 elements
> 
> here I am bit confused which group to select , and i selected 1 group?
> Is it correct??
> Any make me clear about this problem
> Thanks in advance.
> 
> 

Which version of Gromacs are you using?  I recall some weird behavior from 
version 3.3.1(?) that I could never get around.  Version 3.3, for example, 
automatically recognizes all the groups in the index file and calculates the 
order parameters along the chain.

I don't know if 3.3.1(?) allows you to select multiple groups, but that's what 
you'd be after - all the groups in the index should be part of the analysis.

-Justin

> 
> On Thu, 31 Jul 2008 Justin A.Lemkul wrote :
>  >Read about how to create the appropriate index file here:
>  >
>  >http://wiki.gromacs.org/index.php/make_ndx
>  >
>  >There are also several posts in the list archive on how to create the 
> index file correctly.
>  >
>  >-Justin
>  >
>  >minnale wrote:
>  >>  Thanks Justin for your prompt reply with better suggestion
>  >>I have done like this
>  >>1.For index file
>  >>  Selected  > a C34
>  >>  3 34 :128 elements
>  >>  then
>  >>  > a C36
>  >>  4 36 : 128 elements......
>  >>  till C50( only C atoms)
>  >>so
>  >>index file contain
>  >>  [C34]
>  >>  atoms
>  >>  [36]
>  >>  atoms...[C50]
>  >>
>  >>2. then I have typed command like this
>  >>  g_order -f .xtc -s .tpr -o ord.xvg -od scd.xvg -n .ndx
>  >>  asked to select group
>  >>Group    0 (  System) has 14036 elements
>  >>Group    1 (  POPC) has  6656 elements
>  >>Group    2 (    SOL) has  7380 elements
>  >>Group    3 (    C34) has  128 elements
>  >>Group    4 (    C36) has  128 elements
>  >>.
>  >>.
>  >>.
>  >>Group    18 (      C50) has  128 elements
>  >>
>  >>Group  Select a group: 3
>  >>Selected 3: 'C34'
>  >>Reading frame    0 time    0.000 Back Off! I just backed up 
> sg-ang.xvg to ./#sg-ang.xvg.1#
>  >>
>  >>Back Off! I just backed up sk-dist.xvg to ./#sk-dist.xvg.1#
>  >>Last frame      25000 time 5000.000
>  >>gcq#189: "Stay Tuned, We'll Be Right Back" (CNN)
>  >>have I done is correct?
>  >>
>  >>I have doubt that the mentioned -o and -od flags didnt generate .xvg 
> file but without mentioning -Sk and -Sg flags .xvg got generated?
>  >>Can you clear this problem.
>  >>Thanks in advance.                      On Thu, 31 Jul 2008 Justin 
> A.Lemkul wrote :
>  >>  >
>  >>  >
>  >>  >minnale wrote:
>  >>  >>  I want to calculate order parameters of palmitoyl and oleyl 
> chains of POPC which ran it for 5ns, so I have done below mentioned steps.
>  >>  >>1. First I tried for Palmitoyl, so I made .ndx file by using 
> make_ndx command and selected a C34|a 035|a C36.....a C50.
>  >>  >>In index file the palmitoyl chain selected like this 
> C34_O35_C36......C50
>  >>  >>
>  >>  >
>  >>  >You need the index groups to specify each atom separately, and 
> only include carbon atoms.  Your index group will be something like:
>  >>  >
>  >>  >[ C34 ]
>  >>  >(atoms)
>  >>  >[ C36 ]
>  >>  >(atoms)
>  >>  >etc.
>  >>  >[ C50 ]
>  >>  >
>  >>  >>2. This index file feed to g_order command
>  >>  >>    g_order -f .xtc -s .tpr -n palmit_ord.ndx -o order -od 
> scd.xvg -unsat
>  >>  >
>  >>  >There are no unsaturated carbons in a palmitoyl chain.
>  >>  >
>  >>  >-Justin
>  >>  >
>  >>  >>  This programming is running very slowly
>  >>  >>Have I done any mistake here?
>  >>  >>I would be thankful for your help
>  >>  >>  >>
>  >>  >>
>  >>  >>
>  >>  
>  >>------------------------------------------------------------------------
>  >>  >>
>  >>  >>_______________________________________________
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>  >>  >-- ========================================
>  >>  >
>  >>  >Justin A. Lemkul
>  >>  >Graduate Research Assistant
>  >>  >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
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>  >
>  >-- ========================================
>  >
>  >Justin A. Lemkul
>  >Graduate Research Assistant
>  >Department of Biochemistry
>  >Virginia Tech
>  >Blacksburg, VA
>  >jalemkul[at]vt.edu | (540) 231-9080
>  >http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>  >
>  >========================================
> 
> 
> 
> Naukri 
> <http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/www.rediff.com/signature-home.htm/1050715198@Middle5/2212974_2205321/2208023/1?PARTNER=3&OAS_QUERY=null>
> 

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

Justin A. Lemkul
Graduate Research Assistant
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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