Fw: [gmx-users] trjconv in martini

[mohammad agha]

Hi Tsjerk,

Thank you very very much from your help about xtcrev.py script, I did it till end according to you said me before, but unfortunately my first problem about view of 2 micelles was not solved and monomers are dispersed during simulation!!! I don't know why!!!
You helped me very much and thank you very much but may I ask you any suggestion about my problem, please?

Best Regards
Sara




________________________________
 rom: 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: Wednesday, January 11, 2012 1:38 PM
Subject: Re: Fw: [gmx-users] trjconv in martini
 
Hi Sara,

If you give two arguments, it shouldn't do that. './xtcrev.py
input.xtc output.xtc' should work fine. Of course I could've clogged
the script with checking the number of input files and such, and maybe
I will later, but for now it's just a nifty hack :p

Cheers,

Tsjerk

On Wed, Jan 11, 2012 at 11:05 AM, mohammad agha <mra_bu at yahoo.com> wrote:
> Hi Tsjerk,
>
> Thank you very much from your reply. Yes, you're right, I corrected that,
> but now it gave me this error:
>
> Traceback (most recent call last):
>   File "./xtcrev.py", line 68, in <module>
>     o = open(sys.argv[2],"w")
> IndexError: list index out of range
>
> 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: Wednesday, January 11, 2012 12:54 PM
>
> Subject: Re: Fw: [gmx-users] trjconv in martini
>
> 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
>>
>>
>>
>> --
>> gmx-users mailing list    gmx-users at gromacs.org
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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
>
>
>
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
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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
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