SV: SV: SV: [gmx-users] g_order version 4.0.x

[Justin A. Lemkul]

Justin A. Lemkul wrote:
> 
> 
> Sarah Witzke wrote:
>> My .xtc file is 219.41 ns and therefor I thought to just use the last 
>> ~100 ns where my molecules have diffused into the membrane.
>>  
>> I have just run g_order again whitout the -b option: the result is the 
>> same, no order parameters.
>>  
>> My index file consists of just one big group. In that groups are the 
>> carbon atoms of the two lipid chains (and the two carbonyl carbons) 
>> for each of my 128 lipids. When running g_order it reads the .ndx file 
>> like this: 
> 
> That is your problem.  You need individual groups for each distinct 
> carbon along the chain.  For an example for proper creation of these 
> groups, see here:
> 
> http://wiki.gromacs.org/index.php/make_ndx
> 

*Edit* I have gone ahead and created a g_order page.  The information about how 
to create index groups seems to fit better there.  Please refer to the new 
g_order page:

http://wiki.gromacs.org/index.php/g_order

-Justin

> -Justin
> 

-- 
========================================

Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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