Number of atoms to high for mdenergy

From: Marek Dynowski (
Date: Thu Aug 16 2007 - 07:41:51 CDT

Dear NAMD users, I did several simulations with NAMD to calculate the
interaction energies between a protein and a substrate molecule (VDW+elec)
with the MDENERGY tool. With small systems it works fine, but if I try to
calculate the interaction energies of the substrate in a system that contains
about 111'200 atoms then I get the following error meassage at the end of the

MDENERGY> Computing...
*** glibc detected *** free(): invalid pointer: 0x0000000000716aa5 ***

At the end of the program means, that all energies are calculated and after
the last frame is finshed this error meassage occurs. The error did not
depend on the number of frames in the trajectory file but on the number of
atoms in the system. Because if I use a coordinate file that contains only a
single frame instead of a complete trajectory file, the error occurs also.

I've tried to reduce the number of atoms in the system after the simulation by
using the PTRAJ module provided by the AMBER suite, but this crashes also due
to the huge number of atoms. And also with VMD it is not possible to reduce
the number of atoms ("complete molecules") in the trajectory file.

So it seems that there is a problem with the size of the memory that must be
allocated by MDENERGY. And I'm afraid of missing data in the calculations.

Do somebody have an idea how to solve this problem? Till now I couldn't find
any hinds by searching the internet and I'm running out of ideas.

Thanks in advance,

Marek Dynowski.
Here the command that I use to start mdenergy:
mdenergy -dcd 05-Dyn.dcd -amber -nonb -self -sel
selection_mol1 -scnb 0.833333 | grep 'ENERGY:' >mol1-dyn5-self.ene

As I said before, it works for smaller systems.

Marek Dynowski
PhD student
ZMBP, Plant Physiology
University of Tuebingen
Auf der Morgenstelle 1
D-72076 Tübingen
Ph: +49 7071 29 78806

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