amber11 pmemd + LAM-7,1,4/torque

The default optimization flag for pmemd.MPI is -fast, which causes some trouble in our cluster since the torque library doesn't like -static at all. You might already know that -fast is equivalent to "-xHOST -O3 -ipo -no-prec-div -static". My suggestion is to use "-axSTP -O3 -ipo -no-prec-div" instead. The reason for that is compatibility, -xHost also isn't a good optimization flag either. All processors in our cluster are not exactly the same, -xHost is just adding a possibility to mess with.

Ubuntu 10.04 LTS and ifort 11 (x86_64)

Basically you need libstdc++.so.5, thus you can follow the steps in http://www.hackourlives.com/ubuntu-10-04-lucid-lynx-libstdc-so-5/ . My experience on this for my x86_64 virtualbox was that you might not need the 32bit library at all, if you don't have /usr/lib32 .

$ wget http://mirrors.kernel.org/ubuntu/pool/universe/g/gcc-3.3/libstdc++5_3.3.6-17ubuntu1_amd64.deb
$ sudo dpkg --install libstdc++5_3.3.6-17ubuntu1_amd64.deb

lack of ppmtompeg from netpbm package disrupts VMD tutorials

There is no ppmtompeg in current netpbm binary rpm distribution at least for fedora due to legal issue(?). This is going to be very annoying for administrator to deploy workstation for computer lab for molecular simulation. REF: http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/14091.html