AMBER Archive (2003)

Subject: Superimposed trajectory

From: Filip Razga (filip_at_chemi.muni.cz)
Date: Tue Jun 10 2003 - 08:59:06 CDT

Hello,
My name is Filip and I have little question about using Ptraj to create
a superimposed trajectory.

My problem : I want to do a trajectory , which every one snapshot is
mass fitted to the first or reference snapshot, thats mean that the
molecule will be superimposed every snapshot to the reference-by using
Ptraj and create a superimposed trajectory without the rotation of the
molecule.The trajectory will stored the coordinates of the fitted
structure every time step-something like mass weight fitted rmsd, but
without calculating the rmsd values, only stored the fitted coordinates.

Thank you for your help

Filip