[gmx-users] Problems with XTC Files
David van der Spoel
spoel at xray.bmc.uu.se
Sun Dec 2 12:20:13 CET 2001
On Sat, 1 Dec 2001, Christoph Meier wrote:
>Thanks for the advice !
>If there is any way to avoid having to restart a large part of my simulation, I
>would prefer it.
>I just realised that in my last e-mail I didn't actually tell
>you what error message I got - here it is:
>"Floating exception (core dumped)"
>I get this error for all programs which I run on my XTC file.
>Any ideas what the problem could be or whether there are other ways of fixing
>this without having to restart it ?
Problem maybe that something went wrong in writing, but not enough wrong
to crash the simulation. Could be e.g. an NFS disk.
We have no tools to repair xtc files. The only thing you could do is try
to write a program that scans the files for a magic number (the start of
each xtc frame is an integer with value 1995). You'd have to scan the file
byte by byte, and then you should do an extra check to see whether this
really is the start. Maybe it can be built into gmxcheck.
Dr. David van der Spoel, Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576, 75123 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://zorn.bmc.uu.se/~spoel
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