g_chi with the -phi and -psi options appears to use non-standard
definitions of those angles. As best as I can discern from my
measurements with VMD and g_chi,
GROMACS g_chi:
phi: H-N-Ca-C minus 180deg
psi: N-Ca-C-O minus 180deg
the file chi.log lists the atoms that I have outlined above and I am
adding the "minus 180deg" because of my VMD-g_chi comparisons.
However, the numbers work out exactly based on the assumption that
this is what is occurring.
What I thought was standard:
phi: C[i-1]-N-Ca-C
psi: N-Ca-C-N[i+1]
Basing alanine dipeptide dihedral umbrella restraints on my
understanding of the backbone dihedrals and then using g_chi to
determine values from the .xtc for WHAM has in this way lead to a PMF
whose magnitude is too large and that is dependent on the actual force
constant used. I have not yet calculated the actual values directly,
but I assume that this is the problem. I noticed this because when i
plot the dih.rest. energy output from g_energy and scatter plot this
with the actual dihedral value from g_chi for a particular umbrella I
get very significant scatter about the expected parabola.
Perhaps I have my definitions backward. Has anybody else run into
this? I was involved in a couple posts about a month ago regarding
dihedral pmfs and other people seem to be getting appropriate results.
http://www.gromacs.org/pipermail/gmx-users/2007-January/025555.html
Thank you.
Chris.
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