Dear all,
Just finished a long simulation of a protein-protein complex. But when I
visualized the protein with VMD the entire protein changes the center and C
terminal tail of one of the proteins slowly moved out of the water box,
dangling out of the box. I researched and this looked like common problem
when iwrap=1 is used. But my question is does it matter for all the
analysis I just did i.e RMSD, energies,pressure .............? Do I need to
run the entire simulation without iwrap?
On one of the questions in amber list Jason had mentioned that it is just
the visualization problem with vmd when iwrap is used. What do I do to
recenter the protein? Does simply re-centering the protein solves the
problem? or Do I need to rerun the simulation?
&cntrl
imin=0,
irest=1,
ntx=5,
nstlim=40000000,
dt=0.002,
ntf=2,
ntc=2,
ntxo=2,
ioutfm=1,
temp0=300.0,
tempi=300.0,
ntpr=10000,
ntwx=10000,
ntwr=10000,
cut=10.0,
iwrap=1,
ntb=2,
pres0=1.0,
ntp=1,
taup=2.0,
ntr=0,
ntt=3,
gamma_ln=1.0,
ig=-1,
/
Thank you,
RT
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Received on Thu May 19 2016 - 19:30:04 PDT
