Re: A problem with intermediate files

From: Ioana Cozmuta (
Date: Mon Nov 10 2003 - 22:09:20 CST


By default your output files will be written in binary format. Use
binaryrestart no
binaryoutput no

in your NAMD configuration file before running your jobs.

Otherwise you would have to use a converter from binary to ascii on the
machine you've generated those files. Maybe someone else has a better
suggestion about this.

Hope this helps,


On Mon, 10 Nov 2003, Zhilei Chen wrote:

> Hi,
> I was using namd to run a 60ps free simulation. At the end of the simulation,
> I successfully obtained the .dcd file and .log file. Everything is normal. But
> when I try to use the .coor file it generated, I found it only contained some
> strange code that the vmd can't interprete. I checked the other intermediate
> files (.vel, .restart.vel.old, .restart.vel, .restart.coor, .restart.coor.old)
> and all those contained the same strange code and they all have the same file
> size 1,063,600. I am not sure what is the problem. I tried running the script
> again, used a different name, but exactly the same thing happened. All those
> files still have 1,063,600 as the size and have the same mysterious code in
> it. And again, the .dcd file looked normal and I can open it with VMD. I
> examined the .log file, and it didn't have any warning or error message
> concerning writing these intermediate files.
> I need to use the .coor and .vel for my next simulation. Can anyone tell me
> what's the problem?
> zhilei

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