Re: catDCD 32 bit Vs. 64 bit Version

From: Philip Peartree (p.peartree_at_postgrad.manchester.ac.uk)
Date: Sat Feb 02 2008 - 10:21:44 CST

I wrote a tcl script to run in VMD that batch converts from 64 bit to 32 bit dcd... sadly I'm not in the lab so I can't get it, but it's not to difficult tbh, it's pretty quick to do. I'll see if I can dig it up anywhere.

Mr Philip Peartree MSc AMRSC
Computational Enzymology
University of Manchester

----- Original Message -----
From: juneja_at_speakeasy.net
To: "Peter Freddolino" <petefred_at_ks.uiuc.edu>
Cc: namd-l_at_ks.uiuc.edu
Sent: 01 February 2008 23:59:52 o'clock (GMT) Europe/London
Subject: Re: namd-l: catDCD 32 bit Vs. 64 bit Version

Dear Peter,

I would appreciate if you please let me know some solution to convert 64bit dcd to 32bit dcd.

Best Wishes,
Alok

On Fri Feb 1 16:56 , Peter Freddolino sent:

Ahh, my apologies; I didn't realize you were using charmm for your MD, I
thought it was namd.
I'm not very familiar with the options that charmm uses for writing its
dcds. I'll pass this along to the maintainers of the molfile plugins to
see what they have to say. In the meantime, do you have a working option
for converting to 32 bit dcds?

Best,
Peter

juneja_at_speakeasy.net wrote:
> Dear Peter,
>
> I am producing this dcd from charmm on AMD Opteron(tm) Processor 2222
> 64bit machine. I try to get the number of frames in the dcd so I use
> the catDCD to find it (although I knew how many frames I will have in
> my charmm produced dcd). The output of catDCD is as follows:
>
> - - - - - -
> CatDCD 4.0
> dcdplugin) detected CHARMM -i8 64-bit DCD file of native endianness
> dcdplugin) CHARMM format DCD file (also NAMD 2.1 and later)
> dcdplugin) Warning: DCD header claims 525000 frames, file size
> indicates there are actually 554166 frames
> dcdplugin) detected CHARMM -i8 64-bit DCD file of native endianness
> dcdplugin) CHARMM format DCD file (also NAMD 2.1 and later)
> dcdplugin) Warning: DCD header claims 525000 frames, file size
> indicates there are actually 554166 frames
> Opened file 'dyna.dcd' for reading.
> Read 554166 frames from file dyna.dcd.
> Total frames: 554166
> CatDCD exited normally.
> - - - - - -
>
> If you look to the above output you will see the conflict. Actually in
> charmm I am producing 525000 frames however catDCD shows that there
> exists 554166 frames (which I believe is wrong). For the sake of check
> I converted this charmm generated 64bit dcd (dyna.dcd) to 32bit dcd
> (dyna_32bit.dcd) and then read it with catDCD and I figure out that
> everything goes fine and I get the following output:
>
> - - - - - -
> CatDCD 4.0
> dcdplugin) detected standard 32-bit DCD file of native endianness
> dcdplugin) CHARMM format DCD file (also NAMD 2.1 and later)
> dcdplugin) detected standard 32-bit DCD file of native endianness
> dcdplugin) CHARMM format DCD file (also NAMD 2.1 and later)
> Opened file 'dyna_32bit.dcd' for reading.
> Read 525000 frames from file dyna_32bit.dcd.
> Total frames: 525000
> CatDCD exited normally.
> - - - - - -
>
> Best
> -Alok
>
>
> On Thu Jan 31 20:26 , Peter Freddolino sent:
>
> Hi Alok,
> I don't think this is likely to be the problem if you're just
> working on
> an amd64; I routinely transition between dcds produced by 64-bit and
> 32-bit machines without difficulty. namd should write with the same
> precision in either case. Could you specify where and how you
> produced
> the dcd, where you're trying to read it, and what the expected and
> actual number of frames are? The only time I'm aware of there being
> portability problems with dcds is where there's a change in endianism
> between machines, or when you're using AIX (see the discussion at
> http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/3332.html
> www.ks.uiuc.edu %2FResearch%2Fnamd%2Fmailing_list%2Fnamd-l%2F3332.html>).
>
> Best,
> Peter
>
> Alok Juneja wrote:
> > Hello Everybody,
> >
> > I have written 64 bit dcd file and now ask catDCD to figure out the
> > details of the dcd file. Though catDCD reads the 64 bit dcd but
> shows
> > wrong number of frames in contrast to the correct number of frames
> > shown in the header of dcd. I believe this is all because of
> problems
> > related to reading of 64 bit dcd file by 32 bit catDCD. Is there any
> > way to solve this problem. Is 64 bit version of catDCD is available.
> > Just to intimate that I am using AMD Athlon(tm) 64 Processor.
> >
> >
> > Best Wishes,
> > Alok
>
>

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