minnale wrote:
Thanks to Justin for his suggestion
I tried the way mentioned in http://wiki.gromacs.org/index.php/make_ndx.
I made index file with seperate groups and feed to g_order command
g_order -f .xtc -s .tpr -od scd.xvg -o ord -n .ndx
Group 0 ( C34) has 128 elements
Group 1 ( C36) has 128 elements
Group 2 ( C37) has 128 elements
.
.
.
.
.
.
. and so on till Group 15 ( C50) has 128 elements
here I am bit confused which group to select , and i selected 1 group?
Is it correct??
Any make me clear about this problem
Thanks in advance.
Which version of Gromacs are you using? I recall some weird behavior from
version 3.3.1(?) that I could never get around. Version 3.3, for example,
automatically recognizes all the groups in the index file and calculates the
order parameters along the chain.
I don't know if 3.3.1(?) allows you to select multiple groups, but that's what
you'd be after - all the groups in the index should be part of the analysis.
-Justin
On Thu, 31 Jul 2008 Justin A.Lemkul wrote :
>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
>> >> >>
>> >>
>> >>
>>
>>------------------------------------------------------------------------
>> >>
>> >>_______________________________________________
>> >>gmx-users mailing list [email protected]
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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
>> >
>> >========================================
>>
>>
>>
>>
>>------------------------------------------------------------------------
>>
>>_______________________________________________
>>gmx-users mailing list [email protected]
>>http://www.gromacs.org/mailman/listinfo/gmx-users
>>Please search the archive at http://www.gromacs.org/search before
posting!
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interface or send it to [EMAIL PROTECTED]
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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
>
>========================================
Naukri
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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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