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