Fw: [gmx-users] trjconv in martini

[Tsjerk Wassenaar]

Hi Sara,

That can only happen if the input file is empty.
But I now see that the output file should be given as second argument,
so it should be

./xtcrev.py input.xtc output.xtc

rather than

./xtcrev.py input.xtc > output.xtc

The latter will actually result in an empty xtc file. Maybe that's the
cause of the problem? Sorry about that.

Cheers,

Tsjerk

On Tue, Jan 10, 2012 at 6:38 PM, mohammad agha <mra_bu at yahoo.com> wrote:
> 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
> Sara
> ________________________________
> 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
> matter.
>
> Good luck,
>
> Tsjerk
>
>
>
> --
> 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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-- 
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