AMBER Archive (2006)

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

From: Carlos Simmerling (
Date: Tue Aug 01 2006 - 13:13:07 CDT

check the ptraj section of the manual, you can
specify range and stride through the frames in the trajin command.

Xiaojian Deng wrote:

> 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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