[gmx-users] Order parameters of lipid

[Justin A. Lemkul]

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
>  >
>  >========================================
> 
> 
> 
> 
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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

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