Resolved or unresolved issues, by version. New issues and versions added to top. Please let us know if you come across an easily reproducible example of any of the unresolved issues below. Also feel free to add workarounds or other insights below.
Please note that when a bug is "fixed" that means it should not appear in newer versions, not that we have rebuilt all of the binaries on the download page. If you need the fix for a bug in the most recent version you will need to download the nightly build or compile from the source code in CVS.
Beginning with 2.11b1 (days before the release) DCD trajectory files written in parallel by memory optimized builds are corrupted (only contain data from a single writer). Fixed in CVS.
Minimizer may appear to hang while stuck in an infinite loop. Fixed in CVS.
Targetted MD was applying the right forces to the wrong atoms for parallel runs. Fixed in CVS.
If you have switching off and don't specify a cutoff distance you will get a random value for cutoff (typically zero but possibly any other floating point number). Always specify cutoff distances. Fixed in CVS.
When using the coorfile command to read a trajectory containing periodic cell coordinates (e.g., when using the "NAMD Energy" plugin of VMD) the alpha and gamma angles are swapped. This is only a problem for non-orthogonal (e.g., hexagonal) periodic cells. Fixed in CVS.
Parallel runs will often crash (segment fault) during startup phase 1 when CMAP crossterms are present in the psf file. Fixed.
NAMD will report zero energies on pair interaction runs when reading a DCD trajectory file that contains periodic cell information if the config file does not specify periodic boundaries. This is easy to spot if the "PATCH GRID IS" line on startup doesn't say "(PERIODIC)" in all three dimensions, but you see volume and pressure in the energy output. Fixed.
NAMD will hang during the first timestep if any of the "global" force methods such as TclForces, IMD, SMD, or conformational free energy are used and more than 64 processors are being used and the simulation has more patches (see the patch grid dimension output and multiply) than processors. Fixed.
Net forces from pair interactions calculations (pairInteraction on) are incorrect. Forces are accumulated with essentially random signs that are consistent between runs. For a single pair of atoms, this may produce a sign error, while for larger numbers of atoms the net forces are effectively random. The calculated interaction energies are correct, but the forces are meaningless. Fixed.
There is a report of "BUG ALERT: Stray PME grid charges detected!" after 40,000 steps when running Linux-i686 on an Opteron cluster, but not for Linux-i686-TCP.
There is a similar report of errors from Linux-i686 but not from Linux-i686-TCP. I was able to reproduce this locally. Adding +netpoll to the namd2 command line for Linux-i686 results in stable operation. PPL is looking into it.
Eventually resolved as an icc issue, and the following text added to release notes:
If you are building a non-smp, non-tcp version of net-linux with the Intel icc compiler you will need to disable optimization for some files to avoid crashes in the communication interrupt handler. The smp and tcp builds use polling instead of interrupts and therefore are not affected. Adding +netpoll to the namd2 command line also avoids the bug, but this option reduces performance in many cases. These commands recompile the necessary files without optmization:
cd charm/net-linux-icc /bin/rm tmp/sockRoutines.o /bin/rm lib/libconv-cplus-* ( cd tmp; make charm++ OPTS="-O0 -DCMK_OPTIMIZE=1" )
There are reports of floating point exceptions, infinite loops, or NaN (not a number) in output when very small systems are minimized for 10,000 steps or so. Not sure which platforms are affected, but I can get a divide by zero due to floating point underflow on Alpha. Fixed by comparing divisor to zero first.
These meaningless warnings are printed, once per processor:
Warning: FOUND 0 ATOMS WITH ZERO OR NEGATIVE MASSES! CHANGED TO 0.001 Warning: FOUND 0 ATOMS WITH ZERO OR NEGATIVE MASSES! CHANGED TO 0.001 Warning: FOUND 0 ATOMS WITH ZERO OR NEGATIVE MASSES! CHANGED TO 0.001 Warning: FOUND 0 ATOMS WITH ZERO OR NEGATIVE MASSES! CHANGED TO 0.001 ...
Please ignore these. Simple missing logic, fixed.
Dies during startup for Amber rigid waters with:
FATAL ERROR: CAN'T FIND BOND PARAMETERS FOR BOND HW - HW IN PARAMETER FILES
NAMD 2.0 beta 3
NAMD 2.0 beta 2