[gmx-users] cutting the trajectory in small subtrajectories

[Alan Dodd]

Yes, that's exactly what the first reply was telling you.  The option is "stride", I believe.


----- Original Message ----
From: serdar durdagi <durdagis at yahoo.de>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Tuesday, May 13, 2008 8:44:37 AM
Subject: Re: [gmx-users] cutting the trajectory in small subtrajectories


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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