AMBER Archive (2006)

Subject: AMBER: Ignoring every other frame in a .crd trajectory in Ptraj

From: Xiaojian Deng (xjd002_at_gmail.com)
Date: Tue Aug 01 2006 - 12:55:31 CDT

Suppose I split a 2 ns sander simulation into two parts.

Part 1 has dt = 0.002, nstlim = 50000, ntpr = 100

Part 2 has dt = 0.001, nstlim = 100000, ntpr = 100

The coordinate files for each part, respectively, are crd.1 and crd.2. Even
though each output coordinate file represents 1ns of the simulation, the
second one is twice as large because the dt is half the size. Now if I
decide I want to output the RMSD values into a file (that I'll plot), I
could create an input file for PTRAJ like:

trajin crd.1
trajin crd.2
rmsd first out rmsd.txt

But obviously, when I try to plot rmsd.txt, the scaling would be off,
meaning the last 2/3 of the graph would only represent the second half of
the simulation. Is there any way that I can specify in ptraj to extract
only every other frame in crd.2 to avoid this pitfall? Thanks.

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