[gmx-users] S**2 order parameter from a trajectory

Ramon Crehuet rcsqtc at iqac.csic.es
Thu Nov 5 16:51:44 CET 2015

Dear all,
I would like to calculate the S**2 order parameter from the rotational 
correlation function. Following the documentation and serveral previous 
recommendations in the list, I have done the following:

1. Create an index file of pairs of atoms N H with gmx make_ndx -f run2.tpr -o 
nh and selecting NH pairs

2. Remove translation and rotation from my trajectory with:
gmx trjconv -fit rot+trans -s run2.tpr -f run2.trr -o run2_norottrans.xtc

3. Calculate the correlation functions with:
gmx rotacf -d -noaver -n nh -P 2 -f run2_norottrans.xtc -s run2.tpr -o 

I have a couple of questions:

1. In step 3, is it ok to use the index file from  run2.tpr of the whole system 
(with water and ions) and apply it to an xtc that was generated only for the 
protein group (in step 2)?

2. My correlation functions do not decay to zero. They all start at 1 and 
*increase* to 1.0025. Is this normal? I don't think I can fit that to a model 
free with two parameters S**2 + (1-S**2)*exp(-t/tau) ...

Thanks in advance,


Ramon Crehuet
Cientific Titular (Assistant Professor)
Institute of Advanced Chemistry of Catalonia
Tel. +34 934006116
Jordi Girona 18-26
08034 Barcelona (Spain)

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