Chih-Ying Lin wrote:
HI
g_chi is designed to help user to calculate the dihedral angles.
I have an organic compound and as the manual describes that .gro ,
.trr and ssdump.dat are the required input files to compute and
collect the dihedral angles with time.
g_chi is for use with the peptide backbone, according to the
documentation, so I don't know how applicable it necessarily is to your
situation.
You might be better off using g_angle with an appropriate index group
for the dihedral(s) of interest. I have had success using it with small
organic molecules.
-Justin
For my case, .gro and .trr files are ready.
How to prepare for ssdump.dat?
Also, how do i tell gromacs the calculate the specific dihedral angles
with time for me??
I did not fully understand the manual's description.
thank you
Lin
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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