Hi, 2013/2/11 massimo sandal <[email protected]>: > Hi, > > I am trying to run the thermoforce correction for a custom solvent+molecule > system. I am using basically the same settings.xml as of the spce/tf > tutorial of VOTCA 1.2.3. I can run the tutorial without problems, but when I > try to do the same on another system, I have two issues: 0.) There is an AdResS bug in the gromacs 4.6, please make sure you are using a version which includes: <https://gerrit.gromacs.org/#/c/2120/>
> 1) What is the actual meaning of the following settings.xml parameters and > how do I calculate them for my own system? > <!-- thermodynmic force: apply in this range --> > <min>1.4</min> > <max>3.1</max> > <step>0.01</step> > <!--spline:offset beyond the hyrbid zone to take into account for > fitting the spline--> > <tf> > <spline_start>0.9</spline_start> > <spline_end>3.6</spline_end> > <spline_step>0.4</spline_step> > <molname>SOL</molname> > <prefactor>0.01382</prefactor> > </tf> Section 5.7 of the manual explains these parameters, but in short we do a spline fit thorough the density, for which you can specify it's own gird. Usually you want to have coarser grid (otherwise the fit is no fit) and a bigger region to avoid artifact and the boundaries of the tf. > > > 2) When I try to calculate the thermoforce correction, csg_inverse stops > immediately with the following error (from inverse.log): > > ------------------------ > Prepare (dir step_000) > ------------------------ > cp_from_main_dir: 'adress_spce.itp grompp.mdp topol.top table.xvg index.ndx > table_XX_XX.xvg' > Running critical command 'pushd > /home/massimo/gromacs/cg-adress-tests/adress-uim-20130108/thermoforce' > ~/gromacs/cg-adress-tests/adress-uim-20130108/thermoforce > ~/gromacs/cg-adress-tests/adress-uim-20130108/thermoforce/step_000 > Running critical command 'cp adress_spce.itp grompp.mdp topol.top table.xvg > index.ndx table_XX_XX.xvg > /home/massimo/gromacs/cg-adress-tests/adress-uim-20130108/thermoforce/step_000' > Running critical command 'popd' > ~/gromacs/cg-adress-tests/adress-uim-20130108/thermoforce/step_000 > Running subscript 'prepare_generic.sh' (from tags prepare tf) dir > /home/massimo/gromacs/votca/votca/share/votca/scripts/inverse > For all bonded > For all non-bonded > for_all: run 'do_external prepare_single tf' > Running subscript 'prepare_generic_single.sh' (from tags prepare_single tf) > dir /home/massimo/gromacs/votca/votca/share/votca/scripts/inverse > Using initial guess from dist dens.SOL.xvg for SOL > cp_from_main_dir: 'dens.SOL.xvg' to 'SOL.dist.tgt' > Running critical command 'pushd > /home/massimo/gromacs/cg-adress-tests/adress-uim-20130108/thermoforce' > ~/gromacs/cg-adress-tests/adress-uim-20130108/thermoforce > ~/gromacs/cg-adress-tests/adress-uim-20130108/thermoforce/step_000 > Running critical command 'cp dens.SOL.xvg > /home/massimo/gromacs/cg-adress-tests/adress-uim-20130108/thermoforce/step_000/SOL.dist.tgt' > Running critical command 'popd' > ~/gromacs/cg-adress-tests/adress-uim-20130108/thermoforce/step_000 > Running critical command 'mktemp -u SOL.pot.new.raw.XXX' > Running subscript 'calc_thermforce.sh SOL.dist.tgt SOL.pot.new.raw.jn0' > (from tags calc thermforce) dir > /home/massimo/gromacs/votca/votca/share/votca/scripts/inverse > an error occurred: > property not found: tf > > Callstack: > /home/massimo/gromacs/votca/votca/share/votca/scripts/inverse/inverse.sh - > linenumber 166 > do_external - linenumber 170 in > /home/massimo/gromacs/votca/votca/share/votca/scripts/inverse/functions_common.sh > > /home/massimo/gromacs/votca/votca/share/votca/scripts/inverse/prepare_generic.sh > - linenumber 31 > for_all - linenumber 17 (see 'csg_call --cat function for_all') > do_external - linenumber 18 (see 'csg_call --cat > function do_external') > > /home/massimo/gromacs/votca/votca/share/votca/scripts/inverse/prepare_generic_single.sh > - linenumber 53 > do_external - linenumber 18 (see 'csg_call --cat > function do_external') > > /home/massimo/gromacs/votca/votca/share/votca/scripts/inverse/calc_thermforce.sh > - linenumber 57 > csg_get_interaction_property - > linenumber 79 (see 'csg_call --cat function csg_get_interaction_property') > die - linenumber 2 (see 'csg_call > --cat function die') > ################################################################################################################################################################################################################################################################################################ > # > # > # ERROR: > # > # csg_get_interaction_property: Could not get 'inverse.tf.spline_start' for > interaction with name 'SOL' from > /home/massimo/gromacs/cg-adress-tests/adress-uim-20130108/thermoforce/settings.xml > and no default was found in > /home/massimo/gromacs/votca/votca/share/votca/xml/csg_defaults.xml # > # For details see the logfile > /home/massimo/gromacs/cg-adress-tests/adress-uim-20130108/thermoforce/inverse.log > # > # > # > ################################################################################################################################################################################################################################################################################################ > die: (called from 4468) CSG_MASTER_PID is 3852 > > ---- > Below is settings.xml : > > <cg> > <!-- example for a non-bonded interaction entry --> > <non-bonded> > <!-- name of the index group to calculate density from --> > <name>SOL</name> > <!-- types involved in this interaction --> > > <!-- thermodynmic force: apply in this range --> > <min>1.4</min> > <max>3.1</max> > <step>0.01</step> > <!--spline:offset beyond the hyrbid zone to take into account for > fitting the spline--> > <tf> > <spline_start>0.9</spline_start> > <spline_end>3.6</spline_end> > <spline_step>0.4</spline_step> > <molname>SOL</molname> > <prefactor>0.01382</prefactor> > </tf> > <inverse> > <!-- target distribution --> > <target>dens.SOL.xvg</target> > <!-- update cycles --> > <do_potential>1</do_potential> > <!-- additional post processing of dU before added to potential --> > <post_update></post_update> > <!-- additional post processing of U after dU added to potential --> > <post_add></post_add> > <!-- name of the table for gromacs run --> > <gromacs> > <table>tabletf.xvg</table> > </gromacs> > </inverse> > </non-bonded> > > <!-- general options for inverse script --> > <inverse> > <!-- 300*0.00831451 gromacs units --> > <kBT>2.49435</kBT> > <!-- use gromacs as simulation program --> > <program>gromacs</program> > <!-- gromacs specific options --> > <gromacs> > <grompp><bin>grompp_4.6b2</bin> > </grompp> > <mdrun><command>mpirun -np 8 mdrun_4.6b2</command> > <!-- <opts>-nt 8</opts> --> > </mdrun> > <!-- trash so many frames at the beginning --> > <equi_time>0</equi_time> > <!-- grid for table*.xvg !--> > <table_bins>0.01</table_bins> > <!-- cut the potential at this value (gromacs bug) --> > <pot_max>1000000</pot_max> > <!-- extend the tables to this value --> > <table_end>7.1</table_end> > </gromacs> > <!-- these files are copied for each new run --> > <filelist>adress_spce.itp grompp.mdp topol.top table.xvg index.ndx > table_XX_XX.xvg</filelist> > <!-- do so many iterations --> > <iterations_max>300</iterations_max> > <!-- ibi: inverse biltzmann imc: inverse monte carlo tf: thermody force > --> > <method>tf</method> > <!-- directory for user scripts --> > <scriptdir></scriptdir> > <!-- write log to this file --> > <log_file>inverse.log</log_file> > <!-- write restart step to this file --> > <restart_file>restart_points.log</restart_file> > </inverse> > </cg> In version 1.2.* the tf block has to be inside the non-bonded block (which you did), but in version 1.3 we moved the tf block into the inverse block inside the non-bonded block (as the ft options are only needed for csg_inverse). Anyhow, the error message indicated that you are running a 1.3-dev version, so you will need to use the 1.3-dev version of the tutorials as well. $ ./build --dev csg-tutorials or $ hg clone https://code.google.com/p/votca.csg-tutorials/ should do that for you. Cheers, Christoph > > > ---- > Thanks! > Massimo > > > > -- > You received this message because you are subscribed to the Google Groups > "votca" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to [email protected]. > To post to this group, send email to [email protected]. > Visit this group at http://groups.google.com/group/votca?hl=en. > For more options, visit https://groups.google.com/groups/opt_out. > > -- Christoph Junghans Web: http://www.compphys.de -- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at http://groups.google.com/group/votca?hl=en. For more options, visit https://groups.google.com/groups/opt_out.
