Fw: [gmx-users] trjconv in martini

mohammad agha mra_bu at yahoo.com
Tue Jan 10 18:38:20 CET 2012

Hi Tsjerk,

I know that my question is silly but please help me.

I installed python2.5 on my system, then I ran "./xtcrev.py 1a.xtc > 1a-rev.xtc" but it gave me following error:

Traceback (most recent call last):
  File "./xtcrev.py", line 54, in <module>
    n   = 92 + i(f.read(84)[-4:])       # Size of frame in bytes
  File "./xtcrev.py", line 24, in i
    def i(x): return sum([ord(x[j])<<(24-j*8) for j in range(4)])
IndexError: string index out of range

I know that j is out of range but I don't know that what should I do exactly?

May I ask you to help me, Please?

Best Regards

 From: Tsjerk Wassenaar <tsjerkw at gmail.com>
To: mohammad agha <mra_bu at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org> 
Sent: Saturday, December 31, 2011 3:41 PM
Subject: Re: Fw: [gmx-users] trjconv in martini
Hi Sara,

> # Extract the first part of the trajectory
> trjconv -s md.tpr -f md.trr -n index.ndx -o 1a.xtc -e 19999

That should be -e 199999 :) But you can also use -e 200000. Probably
that is better. I first thought it'd be better to avoid a double
frame, but since trjcat is used to combine the parts again, it doesn't

Good luck,


Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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