AMBER Archive (2009)

Subject: Re: [AMBER] How to split mdcrd files

From: Jason Swails (jason.swails_at_gmail.com)
Date: Sun Nov 15 2009 - 11:35:24 CST

Hi,

You can use the following technique to split up a trajectory file. For a
12000 frame mdcrd that you want to split up into 3 parts, you can do use the
following 3 scripts:

trajin mdcrd 1 4000 1
trajout mdcrd_chunk_1

trajin mdcrd 4001 8000 1
trajout mdcrd_chunk_2

trajin mdcrd 8001 12000 1
trajout mdcrd_chunk_3

One downside of this method is that you'll have to read in the trajectory
file 3 times which could take awhile depending on how big your mdcrd is.
Another option is to only consider every 10 frames when you're doing your
analysis so that it doesn't take quite as much memory:

trajin mdcrd 1 99999999 10
*Enter the rest of your script here*

This will make the computer use 1/10th of the memory needed to process the
whole trajectory.

Good luck!
Jason

On Sun, Nov 15, 2009 at 12:22 PM, shamoon siddiqui <
shamoonsiddiqui_at_gmail.com> wrote:

> Dear All,
> I am trying to do hydrogen bond analysis for my protein dna complex, but
> the
> problem is that my system is very big and my simulation is also of 20 ns.
> That is why ptraj is giving segmentation error, i think because my mdcrd
> file is too much heavy and when i did H-bond analysis with small mdcrd
> file,
> then suceed. So could anyone please tell me how to split mdcrd file into
> several small mdcrd files, i think it is possible with ptraj, but i don't
> know how to do. So please let me know in detail
>
> --
> With best regards
>
> Dr. Shamoon Ahmad Siddiqui
> DBT Postdoctoral Fellow
> Molecular Biophysics Unit
> Indian Institute of Science
> Bangalore-560012, India
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
> 

-- 
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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