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<BR>
Thanks Justin for your prompt reply with better suggestion <BR>
I have done like this<BR>
1.For index file<BR>
Selected <BR>
> a C34<BR>
3 34 :128 elements<BR>
then <BR>
> a C36<BR>
4 36 : 128 elements......<BR>
till C50( only C atoms) <BR>
so<BR>
index file contain<BR>
[C34]<BR>
atoms<BR>
[36]<BR>
atoms...[C50]<BR>
<BR>
2. then I have typed command like this<BR>
g_order -f .xtc -s .tpr -o ord.xvg -od scd.xvg -n .ndx <BR>
asked to select group<BR>
Group 0 ( System) has 14036 elements<BR>
Group 1 ( POPC) has 6656 elements<BR>
Group 2 ( SOL) has 7380 elements<BR>
Group 3 ( C34) has 128 elements<BR>
Group 4 ( C36) has 128 elements<BR>
.<BR>
.<BR>
.<BR>
Group 18 ( C50) has 128 elements<BR>
<BR>
Group Select a group: 3<BR>
Selected 3: 'C34'<BR>
Reading frame 0 time 0.000 <BR>
Back Off! I just backed up sg-ang.xvg to ./#sg-ang.xvg.1#<BR>
<BR>
Back Off! I just backed up sk-dist.xvg to ./#sk-dist.xvg.1#<BR>
Last frame 25000 time 5000.000 <BR>
<BR>
gcq#189: "Stay Tuned, We'll Be Right Back" (CNN) <BR>
<BR>
have I done is correct?<BR>
<BR>
I have doubt that the mentioned -o and -od flags didnt generate .xvg file but without mentioning -Sk and -Sg flags .xvg got generated?<BR>
Can you clear this problem.<BR>
Thanks in advance. <BR>
<BR>
On Thu, 31 Jul 2008 Justin A.Lemkul wrote :<BR>
><BR>
><BR>
>minnale wrote:<BR>
>> 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.<BR>
>>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.<BR>
>>In index file the palmitoyl chain selected like this C34_O35_C36......C50<BR>
>><BR>
><BR>
>You need the index groups to specify each atom separately, and only include carbon atoms. Your index group will be something like:<BR>
><BR>
>[ C34 ]<BR>
>(atoms)<BR>
>[ C36 ]<BR>
>(atoms)<BR>
>etc.<BR>
>[ C50 ]<BR>
><BR>
>>2. This index file feed to g_order command<BR>
>> g_order -f .xtc -s .tpr -n palmit_ord.ndx -o order -od scd.xvg -unsat<BR>
><BR>
>There are no unsaturated carbons in a palmitoyl chain.<BR>
><BR>
>-Justin<BR>
><BR>
>> This programming is running very slowly<BR>
>>Have I done any mistake here?<BR>
>>I would be thankful for your help<BR>
>> <BR>
>><BR>
>><BR>
>><BR>
>>------------------------------------------------------------------------<BR>
>><BR>
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><BR>
>-- ========================================<BR>
><BR>
>Justin A. Lemkul<BR>
>Graduate Research Assistant<BR>
>Department of Biochemistry<BR>
>Virginia Tech<BR>
>Blacksburg, VA<BR>
>jalemkul[at]vt.edu | (540) 231-9080<BR>
>http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<BR>
><BR>
>========================================<BR>
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