[[https://www.charmm.org/ | CHARMM Home]]
====== Tricks ======
  * Don't use "_" when defining arguments, or it error will be out when citing them

====== Basic ======
===== NVT, NPT, CPT =====
<WRAP prewrap>
<code>
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.
</code>
</WRAP>

<code>
http://www.charmm.org/ubbthreads/showflat.php?Cat=0&Number=522&Main=518
</code>

  * examples: http://mmtsb.org/workshops/mmtsb-ctbp_2006/Tutorials/RNA_Tutorial/RNA_Tutorial.html

===== RTF =====
<WRAP prewrap><code>
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.
</code></WRAP>

====== Parallel computing in dual CPU machine ======
  * Install mpich2 from website http://www-unix.mcs.anl.gov/mpi/mpich/index.htm
  * Compile charmm with: ./install.com gnu xlarge M mpich, then answer two questions, the answers are:
    * /usr/local/include
    * /usr/local/lib

====== Installation ======
  * single-core: ./install.com gnu xlarge
  * multiple-core: ./install.com gnu xlarge M
  * xlarge can be replaced w/ xxlarge or huge

  * Install in AMD64 OS (I tried Slamd64 and Ubuntu_amd64)
  * Install intel fortran compiler (I registered an email: snowrecall@gmail.com and SN: ND27-V99TW5N2)
  * But the install.com doesn't work properly. Then try Roy's method: "The solutions on the ubuntuforum.org seem not working for my box correctly, here is my solution."
<WRAP prewrap><code>
  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!
</code></WRAP>
  * compile ifort version of charmm at IA32
<code>
./install.com gnu xlarge ifort (for xlarge mode)
or ./install.com gnu xlarge ifort m mpich (for xlarge-mpi mode)
</code>


====== benchmark ======
  * 6'21//=381// for single CPU of griffin
  * 2'5//=125// for double dual-core of griffin
  * 4'8//=248// for wthr333fa

====== Tutorial ======
  * An excellent self-explained tutorial: http://www.psc.edu/general/software/packages/charmm/tutorial/brooks/input/tutorial.inp (you can go up one level to find more material)
  * http://www.charmmtutorial.org/index.php/CHARMM_Tutorial (pdf version: http://www.charmmtutorial.org/charmmtutorial.pdf)
  * http://www.ch.embnet.org/MD_tutorial/
  * http://www.mdy.univie.ac.at/lehre/charmm/course1/course1.html
  * http://www.bio.unizh.ch/docu/acc_docs/doc/charmm_principles/CHARMm_PrinTOC.doc.html
  * scripts: http://web.bii.a-star.edu.sg/~anita/md/md.htm
  * http://mmtsb.org/workshops/mmtsb-ctbp_2006/Tutorials/WorkshopTutorials_2006.html

====== New version ======
===== Install intel compiler 11 =====
  * download it from https://registrationcenter.intel.com/[[RegCenter:RegisterSNInfo]].aspx?sn=NC5M-Z3FWS7S8&[[EmailID]]=snowrecall%40gmail.com&Sequence=535467 (choose intel64 for our xeon)
  * c++: download from https://registrationcenter.intel.com/[[RegCenter:RegisterSNInfo]].aspx?sn=NRGF-6F5J2N9H&[[EmailID]]=snowrecall%40gmail.com&Sequence=535467
  * http://www.charmm.org/ubbthreads/showflat.php?Cat=0&Board=bug&Number=17014&Searchpage=1&Main=16875&Words=CLK_TCK&topic=&Search=true

====== Tips ======
  * Improper angle: http://www.bio.net/bionet/mm/x-plor/1995-November/000262.html
  * rigid body
<code>
CONS FIX command has been considered, it seems that each domain fixes to a certain position which is meaningless to us. CONS HARM BESTFIT command is also tried, it seems right but it can't reduce the freedom of the system which is also not appropriate.

As far as I know, The SHAPE facility purports to allow rigid object dynamics. However, I don't know how to perform it using aarex.pl in MMTSB.
<!/code>
  * ECHECK error
    * http://www.charmm.org/ubbthreads/showflat.php?Cat=0&Number=405&Main=379
    * http://www.charmm.org/ubbthreads/showflat.php?Cat=0&Number=4587&an=0&page=105

====== 37a2 ======
  * http://www.charmm.org/ubbthreads/ubbthreads.php?ubb=showflat&Number=24449

</code>

======Plant it to orange/violet =======

<code>
sudo su
cd /home/usr/share
rsync -avz charmm/ xuelab@orange:/home/usr/share/


*add the path to ~/.cshrc
# CHARMM
setenv PATH ${PATH}:/home/usr/share/charmm/bin
</code>