AMBER Archive (2009)

Subject: [AMBER] rmsd_ptraj

From: balaji nagarajan (balaji_sethu_at_hotmail.com)
Date: Wed Jul 08 2009 - 23:19:56 CDT

Dear Amber ,

I have looked in to the archive , for calculating rmsd of the trajectory with respect to the first frame
 
but ,

I would like to calculate the rmsd of the trajectory which i have generated in the
simulation , with respect to the model which i built ,

I have minimised and equillibriated my model and now i have the

model.rst file and the trajectory file traj.mdcrd
is it possible to calculate the rmsd of each frame of the trajectory , with this
model file (model.rst ) .

I f so how one should give the ptraj input file

thank you
regards
balaji

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