[gmx-users] Re: readxtc can not get coordinates without jump?

Hu Zhongqiao zhongqiao_hu at nus.edu.sg
Wed May 23 10:43:19 CEST 2007

Hi, Tsjerk

I see, you are right. I checked the coordinates again. Readxtc can give
correct coordinates without jumps.  And it seems that we should be
careful when using trjconv to extract coordinates without jumps.



Message: 1
Date: Mon, 21 May 2007 22:49:03 +0200
From: "Tsjerk Wassenaar" <tsjerkw at gmail.com>
Subject: Re: [gmx-users] readxtc can not get coordinates without jump?
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
	<8ff898150705211349r1347d91fk9f012cafbc1e3a1c at mail.gmail.com>
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Hi Zhongqiao Hu,

Actually, the first procedure will give the wrong results. With option
-b the frames up to that point will be skipped. So the first frame read,
at t(b), will have the jumps removed against the reference structure
given. But in 10 ns, a lot may have happened, making the reference
structure used a very bad reference to remove jumps against.
In stead, with the second procedure, each frame will have the jumps
removed against the previous structure, such that the frame at t(b) will
be reset against t(b-1), which is much more likely to be a proper
reference for that point.

I hope this is a bit clear :S Try to think of what -pbc nojump will do
if there's half a box shift between the reference structure and a frame.



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