From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Dec 13 2011 - 13:44:01 CST

dear domenica,

On Tue, Dec 13, 2011 at 1:13 PM, menica dibenedetto
<domenica.dibenedetto_at_gmail.com> wrote:
> Dear all,
> I used the MDEnergy package and it seems to work. I type this command line:
> mdenergy -pdb 01_wat.pdb -dcd 800frames_finoa68.dcd -amber 01.prmtop -all -o
> out.dat
> ...but at the and I don't have the output file (even it run) and it return
> me the following message-error:
>
> *** glibc detected *** mdenergy: free(): invalid pointer: 0x0000000000822385
> ***
> ======= Backtrace: =========
> [0x4c5536]
> [0x4c9077]
> [0x40aee1]
> [0x4231cc]
> [0x4a5fd0]
> [0x4001b9]
> ======= Memory map: ========
> 00400000-00574000 r-xp 00000000 00:15 1074870026
> /tmp_mnt/home/ippoliti/PROGRAMS/bin/mdenergy.Linux
> 00773000-00775000 rw-p 00173000 00:15 1074870026
> /tmp_mnt/home/ippoliti/PROGRAMS/bin/mdenergy.Linux
> 00775000-06dea000 rw-p 00000000 00:00 0
>  [heap]
> 7f738c000000-7f738c028000 rw-p 00000000 00:00 0
> 7f738c028000-7f7390000000 ---p 00000000 00:00 0
> 7f739378a000-7f7393c0b000 rw-p 00000000 00:00 0
> 7f739464e000-7f73949d3000 rw-p 00000000 00:00 0
> 7f7395058000-7f7395061000 rw-p 00000000 00:00 0
> 7fff914d8000-7fff914ed000 rw-p 00000000 00:00 0
>  [stack]
> 7fff9159d000-7fff9159e000 r-xp 00000000 00:00 0
>  [vdso]
> ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0
>  [vsyscall]
> Aborted
>
> Any suggestion?

looks like a bug in the program or an overly
aggressive compiler that miscompiled your
binary. if it is a memory corruption bug, then
this can be debugged using tools like valgrind.

do you have experience in debugging
and/or programming?

if yes, then you can easily do this yourself.
just ask, if you have a specific question.

if not, you need to provide the smallest(!)
set of files that reproduces this issue (you
can use catdcd to reduce the trajectory for
example) and hope that somebody has the
time to track it down and fix it.
 the original author, jan saam, is no longer
working at the TCBG, so it may take some
effort to convince somebody else to look
into this.

cheers,
    axel.

> Best regards
> Domenica Dibenedetto

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science and Technology
Temple University, Philadelphia PA, USA.