Yulian Gavrilov wrote:
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?
Results are system-dependent. I doubt anyone on the list knows what your
outcome should be. I see nothing wrong with a 4.5-nm RMSF; I've seen higher
values for particularly flexible regions of different proteins.
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?
My gut feeling is no. g_filter modifies the coordinates to give a smooth visual
representation; these are not the actual coordinates produced by the MD
simulation. Just because it gives some aesthetically pleasing result does not
mean that result is right :)
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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