[gmx-users] Order parameters of lipid
Justin A. Lemkul
jalemkul at vt.edu
Fri Aug 1 12:19:33 CEST 2008
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
> >> >> >>
> >> >>
> >> >>
> >>
> >>------------------------------------------------------------------------
> >> >>
> >> >>_______________________________________________
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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
> >
> >========================================
>
>
>
> Naukri
> <http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/www.rediff.com/signature-home.htm/1050715198@Middle5/2212974_2205321/2208023/1?PARTNER=3&OAS_QUERY=null>
>
--
========================================
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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