Re: [AMBER] Trajectory Smoothing

From: Ganesh Krishnan <>
Date: Sun, 18 Apr 2010 13:22:43 -0700 (PDT)

I got it working for both the PBC and non PBC case. What I found was it doesn't care so much for the PBC in the prmtop. Admittedly, I used a non-PBC prmtop, so maybe it won't work if the prmtop had PBCs.

I could use a non-PBC prmtop just fine with both PBC and non-PBC trajectories. Some small changes were required in the mdin file, but that is about it.

-Ganesh Krishnan
the prmtop and traj file need to match exactly. same # atoms, same PBC.
this means if you didn't change the traj file, use the same prmtop as what
generated the trajectory. if you modified the trajectory (stripping atoms,
etc) then you need to modify the prmtop to match exactly.
If the traj file has PBC, then the prmtop needs it too.
so, if you need more help, please be very specific about how you generated
the trajectory and prmtop.

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Received on Sun Apr 18 2010 - 13:30:02 PDT
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