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

[Justin A. Lemkul]

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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