There is a way around with nscm (if you are using amber5 or lower of
course). choose nrun appropriately and set option for removing translation
and rotation motion at the beginning of each run. that should help to some
extent. however, i suspect this is not the best way.
to see if in simulation the protein is travelling indeed, you may just
superimpose w.r.t. one out of a set of conformations and look at the
translation matrix/vector. that should tell the story.
hope this helps.
___________________________________________________________________________
Hello,
First, thank you to Carlos Simmerling and Hai Long for helping me with my
last query. I have another one that I can't figure out from the resources.
It seems that during the simulation my protein travels a lot (all the
atoms move by something like 30 A). However, it is a periodic box simulation,
and when I view the trajectory graphically, I don't see protein rotating
or traslating. Is this an imaging issue? Or do I need to take out rigid-body
motion? I couldn't find such an option in either ptraj or carnal.
I know about NSCM option, but it doesn't work for periodic boundaries,
I don't know why. Any advice would be greatly appreciated.
Best,
Dmitry.
Received on Wed Jul 25 2001 - 09:00:00 PDT
