[gmx-users] Order parameters of lipid

minnale minnale_gnos at rediffmail.com
Thu Jul 31 13:53:44 CEST 2008

Thanks Justin for your prompt reply with better suggestion 
I have done like this
1.For index file
  > a C34
  3 34 :128 elements
  > a C36
  4 36 : 128 elements......
  till C50( only C atoms) 
index file contain

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 ]
>[ C36 ]
>[ 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.
>>   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
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