[gmx-users] How to compute the C-H bond time correlation function for surfactant alkyl chain in micelle with the CHARMM and GROMOS

[sa]

Hi All,

  I would like to compute the time correlation function (tcf) of the
C-H bond vector for all the C-H bonds on the hydrocarbon chain of
surfactants in two micelles simulated with the CHARMM and gromos54A7
force fields. It is not clear to me how do that.

  Below what i did

 1- For the CHARMM simulation I have constructed an index file that
contains all the C H atoms of the alkyl chain, like this :

   aC12 | aH12A | aH12B
   aC13 | aH13A | aH13B
   ...
   ...
  ...
  up to the last methylene group

  aC23| aH23A | aH23B

   It is Correct ?

   2- And use the following command for example for the C12-H bond vector

   g_rotacf_mpi -f micelle_Center_All.xtc -s run_1.tpr -b 110000 -e
130000 -fitfn aexp -d -n micelle_CH_Bonds.ndx -o
micelle_rotacf-C12-P2.xvg < bond_C12.txt ---->

  It is also Correct ?

   I have indeed obtained a correlation function C(t), that i can fit
with 4 exponential but i am not sure if this function is  what i
expect. IF It is ok, i would like to do the same calculations for
surfactants simulated with GROMOS force field. Since in this force
field the apolar hydrogens are not presents, i need to "reconstruct"
them from hydrocarbon chain backbone. Again how to do that ?

   Your guidance would be helpful for me.

   Best

  SA