Dear Gromacs users,
What type of conversion of coordinates is better to use?
I have got 100 ns MD simulations for unmodified ubc7 protein and
ubiquitinated ubc7 protein and converted it's trajectories by using trjconv
and g_filter:
1.*trjconv* -s md100ns.tpr -f traj.xtc -o traj_noPBC_nojump.xtc
-pbc nojump -ur compact -dt 100
2. *g_filter* -f traj.xtc -s md100ns.tpr -oh highpass.xtc -nojump
-b 25000 -dt 100 -fit -n calpha.ndx
I tried RMSF analysis for both variants.
In *trjconv* there are strange jumps (3, 4.5 angstroms) of residues 21, 45,
100, etc. Most of these residues are within loops. It seems normal, that
they move more than others. But 4.5 angstroms – is it ok?
As I understand *g_filter* is used more to make good movies, but without it
I get strange RMSF.
Can I use g_filter instead of using trajconv or after trajconv?
--
Sincerely,
Yulian Gavrilov
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