[gmx-users] g_rama, g_chi for polymer structure
yxc169 at case.edu
Thu Apr 22 07:09:49 CEST 2010
I want to construct the Ramachandran Plot for the molecules I am simulating
-- 100 polyethylene chain (n=16). But when I do $ g_rama, I get "Found 0
phi-psi combinations" message. The problem seems to me that when I ran the
simulation initially, I didn't have dihedral information listed on *.itp
file of my molecule as well as on *.top file. However, I created angle.ndx
file manually with 4 carbon atoms grouped together and can invoke g_angle
command to get other dihedral data I want. I encounter similar error(?)
message "Found 0 phi-psi combinations" while invoking g_chi command.
I think I can play around with g_angle data and get what I want eventually,
but I wonder if I can fully utilize what is already implemented in GROMACS
for my polymer structure.
Thank you for your kind reply in advance.
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