[gmx-users] g_rotacf NH vector relaxation

[Olga Ivchenko]

Dear gromacs users,

I want to calculate NH vector for my ligand simulations using g_rotacf. I
want to ask if I first need to remove rotation and translation degrees of
freedom from the trajectory using the command:
trjconv -f traj.xtc -s 10nsProd_MD.tpr -fit rot+trans -o no_rot_trans.xtc

Also, when I am using this command which group I should select for least
square fit (ligand or the whole system) and a group for output.

The rotation correlation functions  (g_rotacf) output depends on trajectory
type which I have. So C(t) graphics are different if I remove rotation and
translation degrees of freedom.

Please can you advice me on this?




Yours sincerely,
Olga
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20101215/9110ef77/attachment.html>