[gmx-users] Order parameters of lipid
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 :
>> 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
>jalemkul[at]vt.edu | (540) 231-9080
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