[gmx-users] order parameters

David L. Bostick dbostick at physics.unc.edu
Thu Jan 17 17:56:46 CET 2002

Below is an email I sent a while ago to someone asking about order
parameters.  Perhaps it can help you figure out what is happening when you
use g_order..

Hello ,

It's just a guess, but the input index file must contain only the atom
indices for one tail.. i.e. if you have two tails for which you wish to
calculate the order parameter like sn1 or sn2 for a standard phospholipid,
you should put the atom indices for each tail in a single file.  This is
because selection of groups is not interactive like it is for most of the
analysis programs.

Also, if you wish to consider a single hydrocarbon tail, the index file
must not simply have all of the atoms in the hydrocarbon tail.  For
example, there should not simply be one group in the .ndx file which is
called "[ sn1 ]" .  INstead, if you wish to calculate a phospholipid order
parameter profile for an sn1 chain, you list the indices like this..

[ C1 ]
list all atoms in the system at position C1 here
[ C2 ]
list all atoms in the system at position C2 here
[ C3 ]
...  C3 ..
[ C4 ]
etc.. etc.. etc..

I don't know how you organized the input .ndx file, but this is what I can
see might be a problem since there are no explicit instructions in the
manual on how to design the input index file.  If you've done things this
way already, then, I'm not sure what could be wrong.

I hope this helps,

David Bostick					Office: 262 Venable Hall
Dept. of Physics and Astronomy			Phone:  (919)962-0165 
Program in Molecular and Cellular Biophysics 
UNC-Chapel Hill					
CB #3255 Phillips Hall				dbostick at physics.unc.edu	
Chapel Hill, NC 27599	           		http://www.unc.edu/~dbostick	

On Mon, 17 Jan 2000, Peter Fojan wrote:

> Hi all,
> does anyone have any suggestions on how I could extract the order
> parameters for an amino acid side chain from a dynamics trajectory done
> by gromcacs? Any help would be greatly appreciated
> Peter
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