[gmx-users] (no subject)

Justin Lorieau jll2006 at columbia.edu
Wed Jul 24 20:15:46 CEST 2002


    I'm interested in looking at backbone N-H or Ca-H order parameters, and
comparing then to and NMR experiment. I have a couple of questions..

(1) My simulations were done with the GROMACS force field that does not
include the hydrogens explicitly. Although these hydrogens exist in the
trajectory files, can I accurately get good rotational autocorralation data
from these?

(2) I'm using the g_rotacf program to do my analysis, looking at individual
N-H bonds at specific residues (using the '-d' parameter). Is there an
easier way to extract a list of rotational autocorrelation times for a type
of bond (ex: backbone N-H bonds) or backbone model-free order parameters?

I appreciate any advice and suggestions, thanks.


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