[gmx-users] g_confrms

[Mark Abraham]

leila karami wrote:
> Hi
>  
> I used command : [g_confrms -f1 initial.gro  -f2 final.gro -n1 1.ndx -n2 
> 2.ndx -o fit.pdb]   to obtain superimposed structure of initial and 
> final structures. I saw fit.pdb file by vmd but fit.pdb obtained was 
> very mixed,busy and unclear.

This is what VMD representations are for. If you don't want atomistic 
detail, then choose tube, or ribbon or something.

Mark