Skip to content

Commit

Permalink
fixed various issues, closes #38, closes #36, closes #21, closes #20,…
Browse files Browse the repository at this point in the history
… closes #19
  • Loading branch information
oostenbrink committed Jan 10, 2018
1 parent d782372 commit bfdd511
Show file tree
Hide file tree
Showing 10 changed files with 1,835 additions and 907 deletions.
3 changes: 3 additions & 0 deletions gromos++/contrib/0index_contrib.doxy
Original file line number Diff line number Diff line change
Expand Up @@ -36,6 +36,7 @@
* - @ref crossdih_top
* - @ref distmat calculate a distance matrix between structures
* - @ref dipole_pot calculate the potential from water dipoles at a certain location
* - @ref eds_mult_all calculates the parameters s and EiR iteratively for multiple EDS states
* - @ref ener_rplc nonbonded energies after replacement of atoms
* - @ref espmap calculates the vacuum electrostatic potential around a group of atoms
* - @ref force calculates the LJ and CRF force between two groups of atoms
Expand All @@ -51,10 +52,12 @@
* - @ref model models atom positions based on expressions
* - @ref prep_bb prepares a building block
* - @ref renumber re-assigns force field types in building blocks
* - @ref rmsd_cmp calculates atom-positional root-mean-square deviations between two trajectories
* - @ref rottemp calculates temparature distributions
* - @ref saltbridge monitors the occurrence of saltbridges
* - @ref shake applies the SHAKE algorithm to a trajectory
* - @ref stacking monitors the occurrence of stacking residues
* - @ref stat_ana calculates statistical quantities such as averages, standard deviations, block averaged error estimate and distributions
* - @ref structal threads a topology through a structure
* - @ref fit_rdc
* - @ref top_to_build convert a topology to a building block
Expand Down
8 changes: 7 additions & 1 deletion gromos++/contrib/Makefile.am
Original file line number Diff line number Diff line change
Expand Up @@ -47,7 +47,10 @@ bin_PROGRAMS = \
ener_test\
force\
mut_top\
mod_top
mod_top\
rmsd_cmp\
eds_mult_all\
stat_ana

aggregates_SOURCES = aggregates.cc
rottemp_SOURCES = rottemp.cc
Expand Down Expand Up @@ -92,6 +95,9 @@ ener_test_SOURCES = ener_test.cc
force_SOURCES = force.cc
mut_top_SOURCES = mut_top.cc
mod_top_SOURCES = mod_top.cc
rmsd_cmp_SOURCES = rmsd_cmp.cc
eds_mult_all_SOURCES = eds_mult_all.cc
stat_ana_SOURCES = stat_ana.cc

LDADD = $(top_builddir)/src/libgromos.la

Expand Down
File renamed without changes.
File renamed without changes.
Original file line number Diff line number Diff line change
Expand Up @@ -19,10 +19,12 @@
* If distributions are requested (\@dist) start and end values and the number of
* bins have to be given for every column.
*
* Note that program @ref tcf can do the same kind of analysis.
*
* <b>arguments:</b>
* <table border=0 cellpadding=0>
* <tr><td> \@in</td><td>&lt;data file&gt; </td></tr>
* <tr><td>[\@dist/td><td>&lt;start, end, bins for every columngt;]</td></tr>
* <tr><td>[\@dist</td><td>&lt;start, end, bins for every column&gt;]</td></tr>
* </table>
*
* Example:
Expand Down
2,713 changes: 1,815 additions & 898 deletions gromos++/doc/doxygen.conf.in

Large diffs are not rendered by default.

2 changes: 0 additions & 2 deletions gromos++/programs/0index.doxy
Original file line number Diff line number Diff line change
Expand Up @@ -123,7 +123,6 @@
* - @ref r_real_factor calculates crystallographic real-space residuals
* - @ref rgyr calculated radius of gyration
* - @ref rmsd calculates atom-positional root-mean-square deviations
* - @ref rmsd_cmp calculates atom-positional root-mean-square deviations between two trajectories
* - @ref rmsdmat calculates the rmsd-matrix for given structures
* - @ref rmsf atom-positional root-mean-square fluctuations
* - @ref rot_rel calculates autocorrelation functions for rotational relaxation times
Expand All @@ -132,7 +131,6 @@
* - @ref shake_analysis Calculate all interactions for a selected set of atoms
* - @ref sim_box solvates a solute in a box of pre-equilibrated solvent
* - @ref solute_entropy takes a coordinate trajectory and calculated the configurational entropy
* - @ref stat_ana calculates statistical quantities such as averages, standard deviations, block averaged error estimate and distributions
* - @ref structure_factor calculates structure factor amplitudes and phases
* - @ref swd calculates the solute weighted distance for solvents
* - @ref tcf calculate distributions and time correlation functions
Expand Down
4 changes: 0 additions & 4 deletions gromos++/programs/Makefile.am
Original file line number Diff line number Diff line change
Expand Up @@ -24,7 +24,6 @@ bin_PROGRAMS = rmsd\
rmsf\
dipole\
rmsdmat\
rmsd_cmp\
cluster\
postcluster\
check_box\
Expand Down Expand Up @@ -86,7 +85,6 @@ bin_PROGRAMS = rmsd\
reweight\
ext_ti_ana\
ext_ti_merge\
stat_ana\
bilayer_dist\
bilayer_oparam\
rep_ana\
Expand Down Expand Up @@ -131,7 +129,6 @@ rmsf_SOURCES = rmsf.cc
dipole_SOURCES = dipole.cc
cluster_SOURCES = cluster.cc
rmsdmat_SOURCES = rmsdmat.cc
rmsd_cmp_SOURCES = rmsd_cmp.cc
postcluster_SOURCES = postcluster.cc
check_box_SOURCES = check_box.cc
make_top_SOURCES = make_top.cc
Expand Down Expand Up @@ -189,7 +186,6 @@ dfmult_SOURCES = dfmult.cc
reweight_SOURCES = reweight.cc
ext_ti_ana_SOURCES = ext_ti_ana.cc
ext_ti_merge_SOURCES = ext_ti_merge.cc
stat_ana_SOURCES = stat_ana.cc
bilayer_dist_SOURCES = bilayer_dist.cc
bilayer_oparam_SOURCES = bilayer_oparam.cc
rep_ana_SOURCES = rep_ana.cc
Expand Down
6 changes: 6 additions & 0 deletions gromos++/programs/com_top.cc
Original file line number Diff line number Diff line change
Expand Up @@ -161,7 +161,13 @@ int main(int argc, char **argv){
else{
toponame=s.substr(s_it+1,s.size());
repeat=atoi(s.substr(0,s_it).c_str());

if(repeat==0){
throw gromos::Exception("com_top", "using " + s.substr(0,s_it) + " in " + iter->second +
" is not allowed\n use program con_top to exchange only force field parameters\n");
}
}

topnum+=repeat;

// read topology
Expand Down
2 changes: 1 addition & 1 deletion gromos++/programs/prep_noe.cc
Original file line number Diff line number Diff line change
Expand Up @@ -19,7 +19,7 @@
* the topology and a library file. The output can be used to apply distance
* restraints during a simulation using programs promd or md, or to analyse a
* molecular trajectory using program @ref noe "noe". For a definition of the
* different types of pseudo- and virtual atoms see volume 2, page XX. In cases
* different types of pseudo- and virtual atoms see volume 2, section 9.4. In cases
* where the library-file specifies a stereospecific CH2 atom (type 4), but
* does not indicate which of the two protons is specified, NOE upper bounds
* are created for both protons. Program @ref post_noe can process the output
Expand Down

0 comments on commit bfdd511

Please sign in to comment.