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

Justin A. Lemkul jalemkul at
Mon Mar 9 23:42:30 CET 2009

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:

*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:


> -Justin


Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at] | (540) 231-9080


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