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campari 2014-04-17 9 weekly downloads
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README.txt 2014-04-17 3.6 kB 44 weekly downloads
README_v1.txt 2014-02-12 6.6 kB 11 weekly downloads
*** WELCOME TO CAMPARI V2 *** Thank you for your interest in our software and research. We sincerely hope you find CAMPARI useful. For user documentation, installation instructions, etc. open the html-documentation in your browser (http://campari.sourceforge.net/index.html), and navigate from there. - The CAMPARI development team *** Update April 17th 2014 *** We have in the meantime collected a number of smaller and/or silent bugs. Rather than uploading fixes for all of them individually, we have packaged a new archive that includes all the fixes and some minimal, cosmetic corrections. The changes are small in size, and it is straightforward to diff individual source files. The list of bugs that could be triggered by CAMPARI is as follows: - When performing analysis of NMR coupling constants - enabled by http://campari.sourceforge.net/keywords.html#ANGCALC - CAMPARI could crash if the first residue under consideration in a molecule was ineligible for this analysis. - When analyzing type-generalized, intramolecular distance distributions in simulations using ensembles with fluctuating particle numbers, the test for physical presence was erroneous. This bug was specific to input modes 2 or 3 for http://campari.sourceforge.net/inputfiles.html#FMCSC_PCCODEFILE and to intramolecular terms. - For replica exchange calculations with a mix of temperature and Hamiltonian parameters as exchange parameters, the analysis potentially printed out via http://campari.sourceforge.net/keywords.html#REOLCALC used incorrect temperature factors in the calculation of the average work and average free energy. This bug had no impact on any replica exchange simulation or on the output for any other type of replica exchange overlap quantity. - When using the DSSP restraint potential - enabled by http://campari.sourceforge.net/keywords.html#SC_DSSP - it was possible to cause a crash by applying it to systems with missing reference atoms other than the backbone amide hydrogen (most likely for simulations of unsupported polypeptide residues or polypeptide caps). - The reporting of box information in structural output was corrected and/or improved for most output formats. - An erroneous field name was fixed in output file http://campari.sourceforge.net/outputfiles.html#STRUCT_CLUSTERING.graphml (geometric edge length). - For simulations in ensembles with fluctuating particle numbers, the visualization script for structural output - http://campari.sourceforge.net/outputfiles.html#basename_VIS.vmd - may have contained an erroneous quotation mark preventing the script from working correctly. - For simulations using custom constraints in Cartesian space by using input mode A for http://campari.sourceforge.net/inputfiles.html#FMCSC_FRZFILE (explicit freezing of x/y/z), drift removal and the associated accounting of the total number of constraints could be incorrect if an entire Cartesian dimension was removed as degrees of freedom (e.g., the z-coordinates of all atoms in the system were frozen). The list of bugs that could be triggered only by modifying CAMPARI and using existing library functions are as follows: - The 0th order B-spline was not handled correctly in subroutine cardBspline(...) in ewald.f90, and the derivatives were not set to zero explicitly for range exceptions. - The field lensnb of custom type scluster was not copied in subroutine copy_cluster(...) in clustering_utils.f90. All the aforementioned issues are fixed in the new archive. We apologize for any inconvenience this may have caused. - The CAMPARI development team
Source: README.txt, updated 2014-04-17