VMD-L Mailing List
From: John Stone (johns_at_ks.uiuc.edu)
Date: Sat Apr 05 2008 - 13:43:21 CDT
- Next message: Yinglong Miao: "How to read specific DCD frames directly in Fortran?"
- Previous message: Peter Freddolino: "Re: How to read specific DCD frames directly in Fortran?"
- In reply to: Yinglong Miao: "How to read specific DCD frames directly in Fortran?"
- Next in thread: Axel Kohlmeyer: "Re: How to read specific DCD frames directly in Fortran?"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]
Yi,
If you're writing your own Fortran code, you might try using
the VMD plugin code via the Fortran bindings that Axel Kohlmeyer
previously contributed. There's some documentation on this here:
http://www.ks.uiuc.edu/Research/vmd/plugins/doxygen/callmolfileplugins.html#callmolfileplugins
The molfile plugins are open source, so you can use them in your own
software...
Cheers,
John Stone
vmd_at_ks.uiuc.edu
On Sat, Apr 05, 2008 at 02:21:53PM -0400, Yinglong Miao wrote:
> Hi,
>
> I have a question about reading big binary DCD files in FORTRAN. In my
> simulations with NAMD, there are cycles in which I want to read two frames
> at the end of the DCD output trajectory for analysis and go back to NAMD to
> continue. The problem is that the size of the DCD file keeps increasing as
> the simulation goes on, and so does the time needed for reading. I am
> wondering whether their are ways to read the last several frames of a DCD
> file directly without going through the big file from the beginning in
> FORTRAN.
>
> I have tried to open the DCD file with position put at the end of the file
> (append for position) and use "backspace" to read the lines I want, but it
> turned out that the backspace doesn't work for unformatted files. I also
> tried reading DCD lines using "direct access", but it seemed that only 1
> record can be accessed. So my question is whether the DCD file supports
> "direct access" reading. Or are there any other ways you know for my
> purpose? I will appreciate it if you can share your experiences with me.
>
> Thanks,
> Long
>
> --
> Yinglong Miao
> Ph.D. Candidate
> Center for Cell and Virus Theory
> Chemistry Department, Indiana University
> 800 E Kirkwood Ave Room C203A, Bloomington, IN 47405
> Tel: 1-812-856-0981
-- NIH Resource for Macromolecular Modeling and Bioinformatics Beckman Institute for Advanced Science and Technology University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801 Email: johns_at_ks.uiuc.edu Phone: 217-244-3349 WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
- Next message: Yinglong Miao: "How to read specific DCD frames directly in Fortran?"
- Previous message: Peter Freddolino: "Re: How to read specific DCD frames directly in Fortran?"
- In reply to: Yinglong Miao: "How to read specific DCD frames directly in Fortran?"
- Next in thread: Axel Kohlmeyer: "Re: How to read specific DCD frames directly in Fortran?"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]