[gmx-users] How to calculate dihedral angle ??

Justin A. Lemkul jalemkul at vt.edu
Mon Jun 30 22:39:17 CEST 2008

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 

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.


> 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


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