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• 18:53, 25 September 2025 Pren talk contribs created page File:REM2023.pdf
• 18:53, 25 September 2025 Pren talk contribs uploaded File:REM2023.pdf
• 23:40, 21 April 2025 Eew947 talk contribs created page Software:links (Created page with "Moved http://biomolmd.org/tinkergpu/index.php/Tinkergpu:Software-list#Arguslab")
• 23:39, 21 April 2025 Eew947 talk contribs created page Research:Svn documentation (Created page with "Subversion is a source control program much like cvs or rcs. It works by keeping track of a main copy of a codebase known as the repository. One checks out a working copy into thier own working directory or codebase. As changes are made to different files in the codebase they are first updated from the repository so that any conflicts can be resolve between conflicting code that some one else may have committed during the time that the changes were made. Next they co...")
• 23:38, 21 April 2025 Eew947 talk contribs created page Research:Programming (Created page with "=Links= *[http://www.intel.com/software/products/compilers/flin/docs/main_for Intel Fortran Compiler Documentation] *[http://www.unix.org.ua/orelly/perl/index.htm Perl Reference] **Also available here: /home/golubkov/Documents/Books/perl_books/index.htm *SVN Documentation *Program Profiling *Neighborlist Tests")
• 23:38, 21 April 2025 Eew947 talk contribs created page Software:Development (Created page with "=Links= * Programming * Corase-grain program subversion * compiler option: add this to F77Flag to intel 9.0 ifort to deal with large arrays (over 2GB static memory) -i-dynamic -mcmodel=large intel math library: LINKFLAGS = -lsvml -Vaxlib -static-libcxa -pg")
• 23:37, 21 April 2025 Eew947 talk contribs created page Software:CGMD (Created page with "==CG code== The latest code (containing bond, angle, torsion, neighbor list, and 1-2 scaling) is located on bme-earth subersion repository. It can be checked out with: =>svn checkout svn+ssh://bme-earth/subversion/tinker-bat Use this syntax even if you are on bme-earth, so the directory is set up properly for when you update and commit from other machines. I also have a working directory in /home/golubkov/tinker-bat that I try to keep up-to-day with the compiled execut...")
• 23:37, 21 April 2025 Eew947 talk contribs created page Software:GB Param (Created page with "==Pavel== crsparam.f int tinker-bat ==Bradley== http://biomol.bme.utexas.edu/wiki/index.php/Research:Dna#GAY-BERNE_PARAMETERIZATION /home/others/hamiltonba/dev/crs-param-cpp/trunk Brad has prgroams to generating all atom dimer configurations at various distances, and at each distance the molecule is rotated about the symmetry axis to get a Boltzmann average all-atom energy for that distance. /home/other/hamiltonab/nuc/vdw2 He has one script for each configuration,...")
• 23:36, 21 April 2025 Eew947 talk contribs created page Research:Ions (Created page with "=Zinc= ==literature== Modeling of Zinc is one of our focuses so we need better understanding of the zinc-protein interactions. I have collect some papers in /opt/reprints/ion-proteins/ZN-pro and …/ZN-MMP In Zn-pro: The zinc-finger.pdf has discussion of various CCCC, CCHC, CCHH complexation with Zn. It suggests that two of the C (cys) lose protons and the total charge of the Zn[CCCC] would be 0. However zn-cystine-expt-solv-lim.pdf suggests that all 4 Cys should l...")
• 23:36, 21 April 2025 Eew947 talk contribs created page Research:Proteomics (Created page with "= Introduction = The Need: It is universally recognized that early detection of cancer and coronary artery disease leads to dramatically improved health outcomes. Yet, there is great scarcity, of minimally invasive, economically feasible approaches to early detection. The ability to obtain early warning information from proteins and other molecules in blood or other biological fluids would represent an epochal advance. However, this approach is extraordinarily difficult...")
• 23:35, 21 April 2025 Eew947 talk contribs created page Research:Peptide (Created page with "* Howto REMD * extract peptide from gromacs * Sai's log ")
• 23:35, 21 April 2025 Eew947 talk contribs created page Research:Coarsegrain (Created page with "=RNA Statistical Potential with psudoatoms = * Pseudo atom based statistical potential (Zhen and Bell) *Research:RNA Statistical Potentials * RNA project 2006 and prior =GB EMP based model = ==GBEMP== *CG project log *coarse_grain_parameter_document *Deriving molecular multipoles consistent with inertial frame *Research...")
• 23:34, 21 April 2025 Eew947 talk contribs created page Research:amber prog tips (Created page with "== VALENCE<br> ==   opbend is included in angle energy<br> ''' in amoeba_interface.f: ''' <br>  call AM_BONDS_eval(crd,frc,ene(1),vir_tensor)<br>  call AM_UREYB_eval(crd,frc,ene(2),vir_tensor)<br>  call AM_REG_ANGLES_eval(crd,frc,ene(3),vir_tensor)<br>  call AM_TRIG_ANGLES_eval(crd,frc,ene(4),vir_tensor)<br>  call AM_OPBEND_ANGLES_eval(crd,frc,ene(5),vir_tensor)<br>  call AM_TORSIONS_eval(crd,frc,ene(6),vir_tensor)<br> ...")
• 23:33, 21 April 2025 Eew947 talk contribs created page Research:amber modification (Created page with "=== nint in sande needs to be replaced by dinit in pmemmd === === Modifying Sander (amber 8 by Darden, in house) to accept coupling parameter (Chona) === Note: The instructions here refer to the source directory in lela.tacc.utexas.edu. Except for changing <AMBER_TOP>, these instructions should be platform-independent. *'''''Go to <AMBER_TOP>/SRC/sander. The sander source files are in ~chona/amoeba/amber06a7l5_p/SRC/sander, so <AMBER_TOP>=~chona/amo...")
• 23:33, 21 April 2025 Eew947 talk contribs created page Research:condor cluster (Created page with "== Running on the Condor cluster == * An example working directory is in ~chona/amoeba/softcore_vdw3 on lela.tacc.utexas.edu. * Prior to submitting the job, make sure that the dynamic libraries can be found by the dynamic linker. This can be done by redefining the environment library LD_LIBRARY_PATH. In bash, lela% export LD_LIBRARY_PATH=.:$LD_LIBRARY_PATH will prepend the current directory to the list of paths searched by ld or ld.so. Then run ldd lela% ldd sander...")