How I may vizualize moleclar motion in Pymol after QMMM dynamics


Clicked A Few Times
I cant find any examples about what kind of files and how QMMM output files may converting in xtc format for Pymol.
After QMMM dynamics I havent trajectory files.
The Analize directive will not work with QMMM output files, because absent trj files after QMMM dynamics. Am I right?
How I may vizualize moleclar motion?

My prep.nw

start protein_dyn
prepare
source protein3_pdbset1.pdb
new_top new_seq
new_rst
modify segment 11 quantum
update lists
ignore
center
orient
solvate cube 6
write protein_dyn.rst
write protein_dyn.pdb
end
task prepare

My dynamics.nw

start protein_dyn
permanent_dir ./permanent_dir/dynamics
scratch_dir ./scratch_dir

md
system protein_dyn
data 50
isotherm
print step 1 stat 10
end

basis
* library "6-31G"
end

scf
vectors output TOP.movecs
print convergence information mulliken ao
maxiter 50
thresh 1.0e-4
end

qmmm
region qmlink
bqzone 2.0
ncycles 2
density espfit
xyz qw
end

task qmmm scf energy
task qmmm scf dynamics


Forum >> NWChem's corner >> QMMM