[gmx-users] superimposed structures

leila karami karami.leila1 at gmail.com
Tue Dec 22 14:00:13 CET 2009

Dear Mark

*(1)* I did following steps for obtaining superimposed structure:

I obtained 0.gro and 5000.gro files by above command

trjconv -f *.xtc -s *.tpr -o n.gro -dump n-1

I concatenated 2 input files ( 0.gro and 5000.gro).

trjcat -f 0.gro 5000.gro -o f.xtc


trjconv -f f.xtc -s *.gro  -o f.pdb -ter -fit progressive -n n.ndx

simulation time was 5000 ps.

*(2)* I used command : [g_confrms -f1 initial.gro  -f2 final.gro -n1 1.ndx
-n2 2.ndx -o fit.pdb -fit]

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.

is my manner true?

which of manner mentioned above is true?
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