From Rick Venable
They are the formal statistical mechanics designations for the ensembles, and imply the system variables that are regulated or conserved. The N stands for constant particle number, which is usually the case.

NVE: constant number (N), volume (V), and energy (E); the sum of kinetic (KE) and potential energy (PE) is conserved, T and P are unregulated

NVT: constant number (N), volume (V), and temperature (T); T is regulated via a thermostat, which typically adds a degree of freedom to the conserved Hamiltonian; for the CPT module in CHARMM, this is a piston whose KE and PE are included in the Hamiltonian; P is unregulated

NPT: as for NVT, but pressure (P) is regulated; again, for the CPT module this is one or more pistons whose KE and PE are added to the Hamiltonian

Other ensembles are needed for systems with planar interfaces, such as those with lipid bilayers.

Residue topology file. Information how a molecule (e.g., water) or building blocks of larger molecules (e.g., amino acids) are built. Each atom of water has an atom-type, a charge, and we also need to specify the connectivity of the atoms. From these data, CHARMM can usually derive information about angles and dihedral angles itself, although one can always specify them by hand.

  1. download the intel fortran compiler from intel's ftp. If you do not know where to go, search for it on google. The complete package has a size of 128MB, and after unzipping, you will find some rpm files.
  2. select the proper rpm for you computer, For Pentium 32bit processors, you can choose intel-ifort9-9.0-031.i386.rpm. Convert it to deb package with alien. I used -k to reserve the version number.
    sudo alien -k intel-ifort9-9.0-031.i386.rpm
  3. install the deb package.
    sudo dpkg -i intel-ifort9*.deb
  4. go to the default installtion directory, which is, normally, /opt/intel. Change the permission of the directory and its subs with chmod so that every user can access it.
    sudo chmod 755 -R intel/
  5. add the following code to your .bashrc.
    # add Intel Compiler environment variables
    #INSTALLDIR is /opt/intel/fc/9.0/
    if [ -z "${PATH}" ]
    then
    PATH="/opt/intel/fc/9.0/bin"; export PATH
    else
    PATH="/opt/intel/fc/9.0/bin:$PATH"; export PATH
    fi

    if [ -z "${LD_LIBRARY_PATH}" ]
    then
    LD_LIBRARY_PATH="/opt/intel/fc/9.0/lib"; export LD_LIBRARY_PATH
    else
    LD_LIBRARY_PATH="/opt/intel/fc/9.0/lib:$LD_LIBRARY_PATH"; export LD_LIBRARY_PATH
    fi

    if [ -z "${MANPATH}" ]
    then
    MANPATH="/opt/intel/fc/9.0/man":$(manpath); export MANPATH
    else
    MANPATH="/opt/intel/fc/9.0/man:${MANPATH}"; export MANPATH
    fi

    if [ -z "${INTEL_LICENSE_FILE}" ]
    then
    INTEL_LICENSE_FILE="/opt/intel/fc/9.0/licenses:/opt/intel/licenses:${HOME}/intel/licenses"; export INTEL_LICENSE_FILE
    else
    INTEL_LICENSE_FILE="${INTEL_LICENSE_FILE}:/opt/intel/fc/9.0/licenses:/opt/intel/licenses: ${HOME}/intel/licenses"; export INTEL_LICENSE_FILE
    fi
  6. reboot your computer and use ifort to compile your source code. Intel fortran compiler can compile much faster fortran programs on Pentium computers than g95 and gfortran. Enjoy!