[gmx-users] cutting the trajectory in small subtrajectories

[Florian Dommert]

Dear Serdar,


 you can find the option for reading every nth frame in VMD (default is
zero, meaning every frame), when loading the xtc-file into the molecule.
If you want to analyse the trajectory and the tool runs out of memory,
there is also the possibility to analyze the whole file part by part.
Therefore the options -b and -e is included in every gromacs tools set
the first and last point in time for analysis, respectively. So you can
analyze long trajectories without any problems.


Best Regards


Flo


serdar durdagi wrote:

> Dear Florian,
>  
> I want to analyze, trajectory files. So, I need all frames.
>  
> by the way, in VMD is there any option to use every 10th or 20th frame?
>  
> Thanks
>  
> Serdar
>
> */Florian Dommert <dommert at fias.uni-frankfurt.de>/* schrieb:
>
>
>     serdar durdagi wrote:
>
>     > Dear all,
>     >
>     > I made a simulation with 2.5 ns (with 12500 frames), when I want to
>     > open this *.xtc file in VMD, it fails. it can read around 50% of
>     > frames and than complains low virtual memory (actually I am
>     using a PC
>     > that has 1GB RAM).
>     Hello,
>
>     if you just want to watch the movie using vmd, don't use every frame,
>     when opening the xtc-file. Perhaps every 10th or 20th is enough
>     and you
>     won't get out of memory.
>
>     Best Regards
>
>     Flo
>
>
>
>     >
>     > Thus, I would like to cut my *.xtc file to small subtrajectory
>     files.
>     > In gromacs manual, it says it is possible with trjconv option
>     together
>     > with sub. But it's not clear how can I give a command let's say to
>     > divide my whole trajectory file to 5 subtrajectories.
>     >
>     > Thank you very much in advance for your comments.
>     >
>     >
>     > Serdar
>     >
>     >
>     >
>     >
>     >
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>
>     -- 
>     Florian Dommert
>     Dipl.-Phys.
>
>     Computational and Theoretical Softmatter & Biophysics group
>
>     Frankfurt Institute for Advanced Studies
>     Johann-Wolfgang-Goethe University
>
>     Ruth-Moufang-Str. 1
>     60438 Frankfurt am Main
>
>     Phone: +49(0)69 / 798 - 47522
>     Fax: +49(0)69 / 798 - 47611
>
>     EMail: dommert at fias.uni-frankfurt.de
>     Home: http://fias.uni-frankfurt.de/~simbio/Florian_Dommert
>
>
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-- 
Florian Dommert
Dipl.-Phys.

Computational and Theoretical Softmatter & Biophysics group

Frankfurt Institute for Advanced Studies
Johann-Wolfgang-Goethe University

Ruth-Moufang-Str. 1
60438 Frankfurt am Main

Phone: +49(0)69 / 798 - 47522
Fax:   +49(0)69 / 798 - 47611

EMail: dommert at fias.uni-frankfurt.de
Home: http://fias.uni-frankfurt.de/~simbio/Florian_Dommert


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