hi all
I am simulating a protein channel in octahedral box and generating my trajectories with iwrap=0 (that is not wrapping ions/waters back into the box). So in that case ions I can do following things:
1) Ions and other molecules of interest for diffusion studies can be done on these trajectories without any modifications on traj files (please correct me!)
2) Now I want to study ions with in protein channels which is also many times reported in papers. I this case I can not use trajectories with iwrap=0 because ions may have diffused far away. In that case how I should image my traj files. I tried these on some restart file:
trajin temp.nc
image
trajout temp.rst restart
and
trajin temp.nc
center :1-25 (1 to 25 represent one molecule)
image
trajout temp.rst restart
and
trajin temp.nc
autoimage :1-25
trajout temp.rst restart
But in all these cases, except autoimage, my molecule looks broken everywhere. But as I said its protein channel I do not have any central residue which can be used in autoimage reference. With autoimage option channel is not in center of box.
thanks
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Received on Mon Jan 27 2014 - 06:30:03 PST
