Re: About matdcd

From: Mert Gür (gurmert_at_gmail.com)
Date: Sun Apr 04 2010 - 04:20:50 CDT

Dear XJ,
I am using this script a lot. With its usual settings it should read every
step. Can you also provide how you call the function?
Firstly you can not load 2034500 frames into Matlab. It would generate a
Matrix which is too large to handle . (I am assuming you dont have a 64 bit
machine with lots lots of ram)

What I suspect is this

I think you are missing something.Maybe you have 2034500 frames in your
simulation. But you have set the dcd writing frequency in your conf file to
500.
In that case you have the coordinates of every 500th step.
Best,
Mert

On Sun, Apr 4, 2010 at 5:23 AM, Gong Xiaojing <gongxiaojing2008_at_yahoo.com>wrote:

> Dear all,
> I met a problem when I used MATLAB to analyse my dcd files.
> There should be total 2034500 frames, I need MATLAB to read each frames.
> But the MATLAB only read every 500 frames.
> When I run the programm, there are the outputing in the begining.
> "
> h =
> fid: 3
> endoffile: 3.0449e+009
> NSET: 4069
> ISTART: 500
> NSAVC: 500
> NAMNF: 0
> charmm: 1
> charmm_extrablock: 1
> charmm_4dims: 0
> DELTA: 0.0409
> N: 62354
> "
>
> I notice NSETxISTART = total 2034500 frames,
> I guess my problem may associate with the value of "ISTART" and "NSAVC"
>
> How can I change the ISTART =1 and NSAVC=1?
>
> I will appreciate it if anybody can give me some suggestions.
>
> Best Wishes,
> XJ
>
>


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