AMBER Archive (2003)

Subject: AMBER: image question

From: Li Ying (bj_0306_at_yahoo.com)
Date: Tue Nov 25 2003 - 12:13:21 CST

Dear Amber Users,
 
I use Ptraj in Amber 7 to calculate the RMSD of the simulation trajectory to the first structure. I used image command in Ptraj input file, but the output of RMSD jumps to about 20 angstroms and back soon, which looks like a image problem.
Here is the Ptraj input file:
trajin x.traj
image
strip :WAT
rms first out x.rms :1-22
go
 
Do I need to image the trajectory in other way? Thanks for your help.
Ying Li

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