Fw: [gmx-users] trjconv in martini

Wed Jan 11 11:42:38 CET 2012

Hi Sara,

You have to understand what is happening. You don't have a static
system. Using -pbc nojump, in combination with xtcrev.py may help you
get a view in which the molecules seem to settle on a specific view or
clustering of your systems, in which you have the micelles. But they
will be dispersed before, and maybe after. If you use -pbc cluster,
the same thing will happen. trjconv will try to form clusters for
every frame, but in some frames there are no clear cut clusters.
Usually you can't have it all, and usually you will have to try
several things. First of all, you have to think of the goal. Is it for
visualization, or is it for further analysis. The needs for these two
are usually different.

Cheers,

Tsjerk

On Wed, Jan 11, 2012 at 11:32 AM, mohammad agha <mra_bu at yahoo.com> wrote:
> 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
>>>
>>>
>>>
>>> --
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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
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>> 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.
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>
>
> --
> 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.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

-- 
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