Alan Dodd wrote:
Yes, I never managed to get a later version of g_order to function properly. I
only ever get the -Sg and -Sk outputs, no matter WHAT I put in the index files.
I've just kept an old version of gromacs on the machine I use for analysis. A
copy of 3.2.1 should be quite easy to download, and will definitely work using
the approach you've been told. I'm pretty sure that if you get it wrong, you
just end up with empty output, so if you get numbers then you're doing it right.
My current GMX version is 3.3.3, and it works just fine, in case you want a
newer, functioning version. I don't know what changes were made, but I just
thought you might like to know.
Incidentally, I always get a sawtooth-shaped curve from my g_order. Anyone
know if this is something simple, like a sampling issue, or indicative of
something more serious? I'm fairly sure I've seen it in published MD work with
bilayers, but that doesn't mean it's right of course.
I've seen both jagged and smooth curves in the literature, with smoother curves
probably being a little more common. I think some of Tieleman's work has
indicated a dip in the order paramters just behind the glycerol backbone,
followed by an increase in order around the plateau region, giving a sort of
jagged plot with respect to the first few carbons.
I guess it would depend largely on your lipid, the parameters used, and the
conditions applied. My DPPC curves using Berger's parameters are generally
pretty smooth.
-Justin
----- Original Message ----
From: Justin A. Lemkul <[EMAIL PROTECTED]>
To: Gromacs Users' List <[email protected]>
Sent: Friday, August 1, 2008 11:19:33 AM
Subject: Re: [gmx-users] Order parameters of lipid
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]
>> >>http://www.gromacs.org/mailman/listinfo/gmx-users
>> >>Please search the archive at http://www.gromacs.org/search before
posting!
>> >>Please don't post (un)subscribe requests to the list. Use the www
interface or send it to [EMAIL PROTECTED]
>> >>Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>> >
>> >-- ========================================
>> >
>> >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!
>>Please don't post (un)subscribe requests to the list. Use the www
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
<http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/www.rediff.com/signature-home.htm/[EMAIL PROTECTED]/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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