2013/7/9 <[email protected]>: > So the script prepare_generic_single.sh prepares empty potential. Please, > see attached files I save BAS-BAS.dist.tgt as BAS-BAS.dist.new and run: $ csg_call --ia-type non-bonded --options settings.xml --ia-name BAS-BAS prepare_single ibi BAS-BAS.pot.new looks good. Then I run: $ csg_call --ia-type non-bonded --options settings.xml --ia-name BAS-BAS convert_potential gromacs BAS-BAS.pot.new table_BAS_BAS.xvg and table_BAS_BAS.xvg looks ok, too.
Using VOTCA 1.2.3: $ csg_call --version csg_call, version 1.2.3 hgid: d8ff5b538018 There might be one problem in your settings.xml file! I would never ever name a target *.dist.new! >>>> >> >> >> > <inverse> >>>> >> >> >> > <target>ACI-ACI.dist.new</target> This might conflict with the dist.new generated inside the IBI iteration. Try to rename your target *.dist.tgt or something. And try to clean up your working directory: $ csg_inverse --options settings.xml clean > > Steven > > > On Tuesday, July 9, 2013 9:20:49 AM UTC+1, [email protected] wrote: >> >> My file which potential is converted to zero: >> >> # This file was created Tue Jul 9 08:47:14 2013 >> # by the following command: >> # g_rdf -f C_300_2100ns_45K.xtc -s em.tpr -o ACI-ACI.dist.new -bin 0.02 -n >> index_RDF.ndx >> # >> # g_rdf is part of G R O M A C S: >> # >> # GROwing Monsters And Cloning Shrimps >> # >> @ title "Radial distribution" >> @ xaxis label "r" >> @ yaxis label "" >> @TYPE xy >> @ subtitle "ACIDIC_r1 - ACIDIC_r2" >> 0 0 >> 0.02 0 >> 0.04 0 >> 0.06 0 >> 0.08 0 >> 0.1 0 >> 0.12 0 >> 0.14 0 >> 0.16 0 >> 0.18 0 >> 0.2 0 >> 0.22 0 >> 0.24 0 >> 0.26 0 >> 0.28 0 >> 0.3 0 >> 0.32 0 >> 0.34 0 >> 0.36 0 >> 0.38 0 >> 0.4 0 >> 0.42 0.428026 >> 0.44 2.73004 >> 0.46 3.56834 >> 0.48 7.86533 >> 0.5 10.2691 >> 0.52 8.93595 >> 0.54 8.28634 >> 0.56 16.8549 >> 0.58 25.1403 >> 0.6 31.8824 >> 0.62 43.6097 >> 0.64 45.1671 >> 0.66 39.6977 >> 0.68 34.2941 >> 0.7 39.4517 >> 0.72 47.0501 >> 0.74 60.2617 >> 0.76 83.1488 >> 0.78 90.1104 >> 0.8 86.841 >> 0.82 113.766 >> 0.84 124.038 >> 0.86 117.723 >> 0.88 122.185 >> 0.9 133.969 >> 0.92 138.468 >> 0.94 136.485 >> 0.96 126.105 >> 0.98 114.327 >> 1 104.815 >> 1.02 89.205 >> 1.04 82.5255 >> 1.06 67.4105 >> 1.08 63.1886 >> 1.1 58.2909 >> 1.12 55.5656 >> 1.14 51.483 >> 1.16 50.7894 >> 1.18 44.9605 >> 1.2 43.0024 >> 1.22 44.0899 >> 1.24 44.8404 >> 1.26 44.4271 >> 1.28 40.0075 >> 1.3 36.8646 >> 1.32 32.5488 >> 1.34 30.4067 >> 1.36 29.3558 >> 1.38 24.9819 >> 1.4 24.2348 >> 1.42 21.909 >> 1.44 20.1757 >> 1.46 20.8667 >> 1.48 18.6171 >> 1.5 16.9829 >> 1.52 14.5778 >> 1.54 13.1508 >> 1.56 11.0781 >> 1.58 9.98262 >> 1.6 9.0561 >> 1.62 7.22253 >> 1.64 6.7386 >> 1.66 7.04308 >> 1.68 6.20748 >> 1.7 6.27133 >> 1.72 5.7434 >> 1.74 5.23803 >> 1.76 4.68082 >> 1.78 4.60007 >> 1.8 4.21872 >> 1.82 3.26017 >> 1.84 3.54656 >> 1.86 2.77218 >> 1.88 3.33315 >> 1.9 3.91185 >> 1.92 3.33912 >> 1.94 3.1703 >> 1.96 3.00764 >> 1.98 3.10127 >> 2 2.8319 >> 2.02 2.29492 >> 2.04 1.88721 >> 2.06 1.95752 >> 2.08 1.25676 >> 2.1 1.54118 >> 2.12 1.2938 >> 2.14 1.10483 >> 2.16 0.712186 >> 2.18 0.413146 >> 2.2 0.171631 >> 2.22 0.168553 >> 2.24 0.105354 >> 2.26 0.0887123 >> 2.28 0.0145271 >> 2.3 0.0428265 >> 2.32 0.0701525 >> 2.34 0.124125 >> 2.36 0.108471 >> 2.38 0.173316 >> 2.4 0.131107 >> 2.42 0.154739 >> 2.44 0.190263 >> 2.46 0.162227 >> 2.48 0.184177 >> 2.5 0.108746 >> 2.52 0.166485 >> 2.54 0.175579 >> 2.56 0.241984 >> 2.58 0.249593 >> 2.6 0.245769 >> 2.62 0.132016 >> 2.64 0.108353 >> 2.66 0.138749 >> 2.68 0.063085 >> 2.7 0.0310773 >> 2.72 0.0408292 >> 2.74 0.0201177 >> 2.76 0.00991358 >> 2.78 0 >> 2.8 0.00963237 >> 2.82 0 >> 2.84 0 >> 2.86 0 >> 2.88 0 >> 2.9 0 >> 2.92 0 >> 2.94 0 >> 2.96 0 >> 2.98 0 >> 3 0 >> 3.02 0 >> 3.04 0 >> 3.06 0 >> 3.08 0 >> 3.1 0 >> 3.12 0 >> 3.14 0 >> 3.16 0 >> 3.18 0 >> 3.2 0 >> 3.22 0 >> 3.24 0 >> 3.26 0 >> 3.28 0 >> 3.3 0 >> 3.32 0 >> 3.34 0 >> 3.36 0 >> 3.38 0 >> 3.4 0 >> 3.42 0 >> 3.44 0 >> 3.46 0 >> 3.48 0 >> 3.5 0 >> 3.52 0 >> 3.54 0 >> 3.56 0 >> 3.58 0 >> 3.6 0 >> 3.62 0 >> 3.64 0 >> 3.66 0 >> 3.68 0 >> 3.7 0 >> 3.72 0 >> 3.74 0 >> 3.76 0 >> 3.78 0 >> 3.8 0 >> 3.82 0 >> 3.84 0 >> 3.86 0 >> 3.88 0 >> 3.9 0 >> 3.92 0 >> 3.94 0 >> 3.96 0 >> 3.98 0 >> 4 0 >> 4.02 0 >> 4.04 0 >> 4.06 0 >> 4.08 0 >> 4.1 0 >> 4.12 0 >> 4.14 0 >> 4.16 0 >> 4.18 0 >> 4.2 0 >> 4.22 0 >> 4.24 0 >> 4.26 0 >> 4.28 0 >> 4.3 0 >> 4.32 0 >> 4.34 0 >> 4.36 0 >> 4.38 0 >> 4.4 0 >> 4.42 0 >> 4.44 0 >> 4.46 0 >> 4.48 0 >> 4.5 0 >> 4.52 0 >> 4.54 0 >> 4.56 0 >> 4.58 0 >> 4.6 0 >> 4.62 0 >> 4.64 0 >> 4.66 0 >> 4.68 0 >> >> >> On Tuesday, July 9, 2013 9:01:59 AM UTC+1, [email protected] wrote: >>> >>> Thank you. >>> The problem I face is that in step 000 some potentials have zero values. >>> Hence in step 001 Votca cannot extrapolate them. No clue why thoose >>> potentials are zero values though... >>> >>> On Monday, July 8, 2013 10:26:41 PM UTC+1, Christoph Junghans wrote: >>>> >>>> 2013/7/8 <[email protected]>: >>>> > >>>> > >>>> > W dniu poniedziałek, 8 lipca 2013 18:00:32 UTC+1 użytkownik Christoph >>>> > Junghans napisał: >>>> >> >>>> >> 2013/7/8 <[email protected]>: >>>> >> > >>>> >> > >>>> >> > W dniu poniedziałek, 8 lipca 2013 16:44:20 UTC+1 użytkownik >>>> >> > Christoph >>>> >> > Junghans napisał: >>>> >> >> >>>> >> >> 2013/7/8 <[email protected]>: >>>> >> >> > >>>> >> >> > >>>> >> >> > W dniu poniedziałek, 8 lipca 2013 14:39:49 UTC+1 użytkownik >>>> >> >> > Christoph >>>> >> >> > Junghans napisał: >>>> >> >> >> >>>> >> >> >> 2013/7/8 <[email protected]>: >>>> >> >> >> > Dear Users, >>>> >> >> >> > >>>> >> >> >> > I am trying to run IBI. I have 5 type of beads: POL, NON, >>>> >> >> >> > GLY, >>>> >> >> >> > ACI, >>>> >> >> >> > BAS >>>> >> >> >> > >>>> >> >> >> > My setting.xml: >>>> >> >> >> > >>>> >> >> >> > <cg> >>>> >> >> >> > <non-bonded> >>>> >> >> >> > <name>ACI-ACI</name> >>>> >> >> >> > <type1>ACI</type1> >>>> >> >> >> > <type2>ACI</type2> >>>> >> >> >> > <!-- dimension + grid spacing of tables for calculations >>>> >> >> >> > --> >>>> >> >> >> > <min>0</min> >>>> >> >> >> > <max>2.0</max> >>>> >> >> >> > <step>0.01</step> >>>> >> >> >> > <inverse> >>>> >> >> >> > <target>ACI-ACI.dist.new</target> >>>> >> >> >> > <!-- update cycles --> >>>> >> >> >> > <do_potential>1</do_potential> >>>> >> >> >> > <post_update></post_update> >>>> >> >> >> > <post_add>convergence</post_add> >>>> >> >> >> > <gromacs> >>>> >> >> >> > <table>table_ACI_ACI.xvg</table> >>>> >> >> >> > </gromacs> >>>> >> >> >> > </inverse> >>>> >> >> >> > </non-bonded> >>>> >> >> >> > >>>> >> >> >> > >>>> >> >> >> > <non-bonded> >>>> >> >> >> > <name>ACI-BAS</name> >>>> >> >> >> > <type1>ACI</type1> >>>> >> >> >> > <type2>BAS</type2> >>>> >> >> >> > <!-- dimension + grid spacing of tables for calculations >>>> >> >> >> > --> >>>> >> >> >> > <min>0</min> >>>> >> >> >> > <max>2.0</max> >>>> >> >> >> > <step>0.01</step> >>>> >> >> >> > <inverse> >>>> >> >> >> > <target>ACI-BAS.dist.new</target> >>>> >> >> >> > <!-- update cycles --> >>>> >> >> >> > <do_potential>1</do_potential> >>>> >> >> >> > <post_update></post_update> >>>> >> >> >> > <post_add>convergence</post_add> >>>> >> >> >> > <gromacs> >>>> >> >> >> > <table>table_ACI_BAS.xvg</table> >>>> >> >> >> > </gromacs> >>>> >> >> >> > </inverse> >>>> >> >> >> > </non-bonded> >>>> >> >> >> > >>>> >> >> >> > >>>> >> >> >> > <non-bonded> >>>> >> >> >> > <name>ACI-GLY</name> >>>> >> >> >> > <type1>ACI</type1> >>>> >> >> >> > <type2>GLY</type2> >>>> >> >> >> > <!-- dimension + grid spacing of tables for calculations >>>> >> >> >> > --> >>>> >> >> >> > <min>0</min> >>>> >> >> >> > <max>2.0</max> >>>> >> >> >> > <step>0.01</step> >>>> >> >> >> > <inverse> >>>> >> >> >> > <target>ACI-GLY.dist.new</target> >>>> >> >> >> > <!-- update cycles --> >>>> >> >> >> > <do_potential>1</do_potential> >>>> >> >> >> > <post_update></post_update> >>>> >> >> >> > <post_add>convergence</post_add> >>>> >> >> >> > <gromacs> >>>> >> >> >> > <table>table_ACI_GLY.xvg</table> >>>> >> >> >> > </gromacs> >>>> >> >> >> > </inverse> >>>> >> >> >> > </non-bonded> >>>> >> >> >> > >>>> >> >> >> > >>>> >> >> >> > <non-bonded> >>>> >> >> >> > <name>ACI-NON</name> >>>> >> >> >> > <type1>ACI</type1> >>>> >> >> >> > <type2>NON</type2> >>>> >> >> >> > <!-- dimension + grid spacing of tables for calculations >>>> >> >> >> > --> >>>> >> >> >> > <min>0</min> >>>> >> >> >> > <max>2.0</max> >>>> >> >> >> > <step>0.01</step> >>>> >> >> >> > <inverse> >>>> >> >> >> > <target>ACI-NON.dist.new</target> >>>> >> >> >> > <!-- update cycles --> >>>> >> >> >> > <do_potential>1</do_potential> >>>> >> >> >> > <post_update></post_update> >>>> >> >> >> > <post_add>convergence</post_add> >>>> >> >> >> > <gromacs> >>>> >> >> >> > <table>table_ACI_NON.xvg</table> >>>> >> >> >> > </gromacs> >>>> >> >> >> > </inverse> >>>> >> >> >> > </non-bonded> >>>> >> >> >> > >>>> >> >> >> > >>>> >> >> >> > >>>> >> >> >> > <non-bonded> >>>> >> >> >> > <name>ACI-POL</name> >>>> >> >> >> > <type1>ACI</type1> >>>> >> >> >> > <type2>POL</type2> >>>> >> >> >> > <!-- dimension + grid spacing of tables for calculations >>>> >> >> >> > --> >>>> >> >> >> > <min>0</min> >>>> >> >> >> > <max>2.0</max> >>>> >> >> >> > <step>0.01</step> >>>> >> >> >> > <inverse> >>>> >> >> >> > <target>ACI-POL.dist.new</target> >>>> >> >> >> > <!-- update cycles --> >>>> >> >> >> > <do_potential>1</do_potential> >>>> >> >> >> > <post_update></post_update> >>>> >> >> >> > <post_add>convergence</post_add> >>>> >> >> >> > <gromacs> >>>> >> >> >> > <table>table_ACI_POL.xvg</table> >>>> >> >> >> > </gromacs> >>>> >> >> >> > </inverse> >>>> >> >> >> > </non-bonded> >>>> >> >> >> > >>>> >> >> >> > >>>> >> >> >> > <non-bonded> >>>> >> >> >> > <name>BAS-BAS</name> >>>> >> >> >> > <type1>BAS</type1> >>>> >> >> >> > <type2>BAS</type2> >>>> >> >> >> > <!-- dimension + grid spacing of tables for calculations >>>> >> >> >> > --> >>>> >> >> >> > <min>0</min> >>>> >> >> >> > <max>2.0</max> >>>> >> >> >> > <step>0.01</step> >>>> >> >> >> > <inverse> >>>> >> >> >> > <target>BAS-BAS.dist.new</target> >>>> >> >> >> > <!-- update cycles --> >>>> >> >> >> > <do_potential>1</do_potential> >>>> >> >> >> > <post_update></post_update> >>>> >> >> >> > <post_add>convergence</post_add> >>>> >> >> >> > <gromacs> >>>> >> >> >> > <table>table_BAS_BAS.xvg</table> >>>> >> >> >> > </gromacs> >>>> >> >> >> > </inverse> >>>> >> >> >> > </non-bonded> >>>> >> >> >> > >>>> >> >> >> > >>>> >> >> >> > <non-bonded> >>>> >> >> >> > <name>BAS-GLY</name> >>>> >> >> >> > <type1>BAS</type1> >>>> >> >> >> > <type2>GLY</type2> >>>> >> >> >> > <!-- dimension + grid spacing of tables for calculations >>>> >> >> >> > --> >>>> >> >> >> > <min>0</min> >>>> >> >> >> > <max>2.0</max> >>>> >> >> >> > <step>0.01</step> >>>> >> >> >> > <inverse> >>>> >> >> >> > <target>BAS-GLY.dist.new</target> >>>> >> >> >> > <!-- update cycles --> >>>> >> >> >> > <do_potential>1</do_potential> >>>> >> >> >> > <post_update></post_update> >>>> >> >> >> > <post_add>convergence</post_add> >>>> >> >> >> > <gromacs> >>>> >> >> >> > <table>table_BAS_GLY.xvg</table> >>>> >> >> >> > </gromacs> >>>> >> >> >> > </inverse> >>>> >> >> >> > </non-bonded> >>>> >> >> >> > >>>> >> >> >> > <non-bonded> >>>> >> >> >> > <name>GLY-GLY</name> >>>> >> >> >> > <type1>GLY</type1> >>>> >> >> >> > <type2>GLY</type2> >>>> >> >> >> > <!-- dimension + grid spacing of tables for calculations >>>> >> >> >> > --> >>>> >> >> >> > <min>0</min> >>>> >> >> >> > <max>2.0</max> >>>> >> >> >> > <step>0.01</step> >>>> >> >> >> > <inverse> >>>> >> >> >> > <target>GLY-GLY.dist.new</target> >>>> >> >> >> > <!-- update cycles --> >>>> >> >> >> > <do_potential>1</do_potential> >>>> >> >> >> > <post_update></post_update> >>>> >> >> >> > <post_add>convergence</post_add> >>>> >> >> >> > <gromacs> >>>> >> >> >> > <table>table_GLY_GLY.xvg</table> >>>> >> >> >> > </gromacs> >>>> >> >> >> > </inverse> >>>> >> >> >> > </non-bonded> >>>> >> >> >> > >>>> >> >> >> > <non-bonded> >>>> >> >> >> > <name>GLY-NON</name> >>>> >> >> >> > <type1>GLY</type1> >>>> >> >> >> > <type2>NON</type2> >>>> >> >> >> > <!-- dimension + grid spacing of tables for calculations >>>> >> >> >> > --> >>>> >> >> >> > <min>0</min> >>>> >> >> >> > <max>2.0</max> >>>> >> >> >> > <step>0.01</step> >>>> >> >> >> > <inverse> >>>> >> >> >> > <target>GLY-NON.dist.new</target> >>>> >> >> >> > <!-- update cycles --> >>>> >> >> >> > <do_potential>1</do_potential> >>>> >> >> >> > <post_update></post_update> >>>> >> >> >> > <post_add>convergence</post_add> >>>> >> >> >> > <gromacs> >>>> >> >> >> > <table>table_GLY_NON.xvg</table> >>>> >> >> >> > </gromacs> >>>> >> >> >> > </inverse> >>>> >> >> >> > </non-bonded> >>>> >> >> >> > >>>> >> >> >> > >>>> >> >> >> > <non-bonded> >>>> >> >> >> > <name>GLY-POL</name> >>>> >> >> >> > <type1>GLY</type1> >>>> >> >> >> > <type2>POL</type2> >>>> >> >> >> > <!-- dimension + grid spacing of tables for calculations >>>> >> >> >> > --> >>>> >> >> >> > <min>0</min> >>>> >> >> >> > <max>2.0</max> >>>> >> >> >> > <step>0.01</step> >>>> >> >> >> > <inverse> >>>> >> >> >> > <target>GLY-POL.dist.new</target> >>>> >> >> >> > <!-- update cycles --> >>>> >> >> >> > <do_potential>1</do_potential> >>>> >> >> >> > <post_update></post_update> >>>> >> >> >> > <post_add>convergence</post_add> >>>> >> >> >> > <gromacs> >>>> >> >> >> > <table>table_GLY_POL.xvg</table> >>>> >> >> >> > </gromacs> >>>> >> >> >> > </inverse> >>>> >> >> >> > </non-bonded> >>>> >> >> >> > >>>> >> >> >> > <non-bonded> >>>> >> >> >> > <name>NON-BAS</name> >>>> >> >> >> > <type1>NON</type1> >>>> >> >> >> > <type2>BAS</type2> >>>> >> >> >> > <!-- dimension + grid spacing of tables for calculations >>>> >> >> >> > --> >>>> >> >> >> > <min>0</min> >>>> >> >> >> > <max>2.0</max> >>>> >> >> >> > <step>0.01</step> >>>> >> >> >> > <inverse> >>>> >> >> >> > <target>NON-BAS.dist.new</target> >>>> >> >> >> > <!-- update cycles --> >>>> >> >> >> > <do_potential>1</do_potential> >>>> >> >> >> > <post_update></post_update> >>>> >> >> >> > <post_add>convergence</post_add> >>>> >> >> >> > <gromacs> >>>> >> >> >> > <table>table_NON_BAS.xvg</table> >>>> >> >> >> > </gromacs> >>>> >> >> >> > </inverse> >>>> >> >> >> > </non-bonded> >>>> >> >> >> > >>>> >> >> >> > <non-bonded> >>>> >> >> >> > <name>NON-NON</name> >>>> >> >> >> > <type1>NON</type1> >>>> >> >> >> > <type2>NON</type2> >>>> >> >> >> > <!-- dimension + grid spacing of tables for calculations >>>> >> >> >> > --> >>>> >> >> >> > <min>0</min> >>>> >> >> >> > <max>2.0</max> >>>> >> >> >> > <step>0.01</step> >>>> >> >> >> > <inverse> >>>> >> >> >> > <target>NON-NON.dist.new</target> >>>> >> >> >> > <!-- update cycles --> >>>> >> >> >> > <do_potential>1</do_potential> >>>> >> >> >> > <post_update></post_update> >>>> >> >> >> > <post_add>convergence</post_add> >>>> >> >> >> > <gromacs> >>>> >> >> >> > <table>table_NON_NON.xvg</table> >>>> >> >> >> > </gromacs> >>>> >> >> >> > </inverse> >>>> >> >> >> > </non-bonded> >>>> >> >> >> > >>>> >> >> >> > <non-bonded> >>>> >> >> >> > <name>POL-BAS</name> >>>> >> >> >> > <type1>POL</type1> >>>> >> >> >> > <type2>BAS</type2> >>>> >> >> >> > <!-- dimension + grid spacing of tables for calculations >>>> >> >> >> > --> >>>> >> >> >> > <min>0</min> >>>> >> >> >> > <max>2.0</max> >>>> >> >> >> > <step>0.01</step> >>>> >> >> >> > <inverse> >>>> >> >> >> > <target>POL-BAS.dist.new</target> >>>> >> >> >> > <!-- update cycles --> >>>> >> >> >> > <do_potential>1</do_potential> >>>> >> >> >> > <post_update></post_update> >>>> >> >> >> > <post_add>convergence</post_add> >>>> >> >> >> > <gromacs> >>>> >> >> >> > <table>table_POL_BAS.xvg</table> >>>> >> >> >> > </gromacs> >>>> >> >> >> > </inverse> >>>> >> >> >> > </non-bonded> >>>> >> >> >> > >>>> >> >> >> > >>>> >> >> >> > <non-bonded> >>>> >> >> >> > <name>POL-NON</name> >>>> >> >> >> > <type1>POL</type1> >>>> >> >> >> > <type2>NON</type2> >>>> >> >> >> > <!-- dimension + grid spacing of tables for calculations >>>> >> >> >> > --> >>>> >> >> >> > <min>0</min> >>>> >> >> >> > <max>2.0</max> >>>> >> >> >> > <step>0.01</step> >>>> >> >> >> > <inverse> >>>> >> >> >> > <target>POL-NON.dist.new</target> >>>> >> >> >> > <!-- update cycles --> >>>> >> >> >> > <do_potential>1</do_potential> >>>> >> >> >> > <post_update></post_update> >>>> >> >> >> > <post_add>convergence</post_add> >>>> >> >> >> > <gromacs> >>>> >> >> >> > <table>table_POL_NON.xvg</table> >>>> >> >> >> > </gromacs> >>>> >> >> >> > </inverse> >>>> >> >> >> > </non-bonded> >>>> >> >> >> > >>>> >> >> >> > <non-bonded> >>>> >> >> >> > <name>POL-POL</name> >>>> >> >> >> > <type1>POL</type1> >>>> >> >> >> > <type2>POL</type2> >>>> >> >> >> > <!-- dimension + grid spacing of tables for calculations >>>> >> >> >> > --> >>>> >> >> >> > <min>0</min> >>>> >> >> >> > <max>2.0</max> >>>> >> >> >> > <step>0.01</step> >>>> >> >> >> > <inverse> >>>> >> >> >> > <target>POL-BAS.dist.new</target> >>>> >> >> >> > <!-- update cycles --> >>>> >> >> >> > <do_potential>1</do_potential> >>>> >> >> >> > <post_update></post_update> >>>> >> >> >> > <post_add>convergence</post_add> >>>> >> >> >> > <gromacs> >>>> >> >> >> > <table>table_POL_POL.xvg</table> >>>> >> >> >> > </gromacs> >>>> >> >> >> > </inverse> >>>> >> >> >> > </non-bonded> >>>> >> >> >> > >>>> >> >> >> > >>>> >> >> >> > <inverse> >>>> >> >> >> > <!-- 300*0.00831451 gromacs units --> >>>> >> >> >> > <kBT>2.49435</kBT> >>>> >> >> >> > <program>gromacs</program> >>>> >> >> >> > <gromacs> >>>> >> >> >> > <equi_time>10</equi_time> >>>> >> >> >> > <table_bins>0.002</table_bins> >>>> >> >> >> > <pot_max>1000000</pot_max> >>>> >> >> >> > <table_end>3.0</table_end> >>>> >> >> >> > </gromacs> >>>> >> >> >> > <filelist>grompp.mdp topol.top table*xvg >>>> >> >> >> > index.ndx</filelist> >>>> >> >> >> > <iterations_max>500</iterations_max> >>>> >> >> >> > <convergence_check>default</convergence_check> >>>> >> >> >> > <convergence_check_options> >>>> >> >> >> > <limit>0.001</limit> >>>> >> >> >> > <name_glob>*.conv</name_glob> >>>> >> >> >> > </convergence_check_options> >>>> >> >> >> > <method>ibi</method> >>>> >> >> >> > <log_file>inverse.log</log_file> >>>> >> >> >> > <restart_file>restart_points.log</restart_file> >>>> >> >> >> > </inverse> >>>> >> >> >> > </cg> >>>> >> >> >> > >>>> >> >> >> > and my grompp.mdp >>>> >> >> >> > >>>> >> >> >> > >>>> >> >> >> > integrator = md >>>> >> >> >> > tinit = 0.0 >>>> >> >> >> > dt = 0.002 >>>> >> >> >> > nsteps = 25000000 ; 50 ns >>>> >> >> >> > nstcomm = 100 >>>> >> >> >> > nstcalcenergy = 100 >>>> >> >> >> > >>>> >> >> >> > nstxout = 0 >>>> >> >> >> > nstvout = 0 >>>> >> >> >> > nstenergy = 0 >>>> >> >> >> > nstlog = 10000 >>>> >> >> >> > nstxtcout = 100 >>>> >> >> >> > energygrps = ACI BAS GLY NON POL >>>> >> >> >> > energygrp_table = ACI ACI ACI BAS ACI GLY ACI NON >>>> >> >> >> > ACI POL >>>> >> >> >> > BAS >>>> >> >> >> > BAS >>>> >> >> >> > BAS GLY GLY GLY GLY NON GLY POL NON BAS NON NON POL BAS POL >>>> >> >> >> > NON >>>> >> >> >> > POL >>>> >> >> >> > POL >>>> >> >> >> > >>>> >> >> >> > >>>> >> >> >> > nstlist = 10 >>>> >> >> >> > ns_type = grid >>>> >> >> >> > pbc = xyz >>>> >> >> >> > rlist = 1.4 >>>> >> >> >> > >>>> >> >> >> > coulombtype = User >>>> >> >> >> > rcoulomb = 1.4 >>>> >> >> >> > >>>> >> >> >> > vdw_type = User >>>> >> >> >> > rvdw_switch = 1.0 >>>> >> >> >> > rvdw = 1.4 >>>> >> >> >> > >>>> >> >> >> > >>>> >> >> >> > tcoupl = V-rescale >>>> >> >> >> > tc_grps = Protein >>>> >> >> >> > tau_t = 0.1 >>>> >> >> >> > ref_t = 300 >>>> >> >> >> > pcoupl = no >>>> >> >> >> > >>>> >> >> >> > gen_vel = yes >>>> >> >> >> > gen_temp = 300 >>>> >> >> >> > gen_seed = -1 >>>> >> >> >> > >>>> >> >> >> > >>>> >> >> >> > constraints = none >>>> >> >> >> > constraint_algorithm = Lincs >>>> >> >> >> > unconstrained_start = no >>>> >> >> >> > lincs_iter = 1 >>>> >> >> >> > lincs_order = 4 >>>> >> >> >> > >>>> >> >> >> > >>>> >> >> >> > >>>> >> >> >> > I am getting an error: get_simulation_setting: could not >>>> >> >> >> > fetch >>>> >> >> >> > table-extension from grompp.mdp and no default given, please >>>> >> >> >> > add >>>> >> >> >> > it >>>> >> >> >> > in >>>> >> >> >> > there >>>> >> >> >> So you need to add the table-extension option to your mdp >>>> >> >> >> file. >>>> >> >> >> table-extension = 2.0 >>>> >> >> >> should work for you. >>>> >> >> > >>>> >> >> > >>>> >> >> > Can you please help with my mdp settings. I set: >>>> >> >> > >>>> >> >> > >>>> >> >> > energygrps = ACI BAS GLY NON POL >>>> >> >> > energygrp_table = ACI ACI ACI BAS ACI GLY ACI NON ACI >>>> >> >> > POL >>>> >> >> > BAS >>>> >> >> > BAS >>>> >> >> > BAS GLY GLY GLY GLY NON GLY POL NON BAS NON NON POL BAS POL NON >>>> >> >> > POL >>>> >> >> > POL >>>> >> >> > table-extension = 2.4 ; its distance beyond the >>>> >> >> > largest >>>> >> >> > cuttoff >>>> >> >> > so should be 2.4 as 1.4 (cuttof) + 2.2 makes the table 3.8 >>>> >> >> > >>>> >> >> > >>>> >> >> > nstlist = 10 >>>> >> >> > ns_type = grid >>>> >> >> > pbc = xyz >>>> >> >> > rlist = 1.4 >>>> >> >> > rlistlong = 1.4 >>>> >> >> > >>>> >> >> > coulombtype = User >>>> >> >> > rcoulomb = 1.4 >>>> >> >> > >>>> >> >> > vdw_type = User >>>> >> >> > rvdw_switch = 1.0 >>>> >> >> > rvdw = 1.4 >>>> >> >> > >>>> >> >> > But then I get error that rvdw < the lenght of the table (3.8 >>>> >> >> > nm) >>>> >> >> > which >>>> >> >> > makes sense. If I then set up the rlistlong and rvdw to 3.8 >>>> >> >> > mdrun >>>> >> >> > gives >>>> >> >> > an >>>> >> >> > error: "Tables in file table_ACI_ACI.xvg not long enough for >>>> >> >> > cut-off: >>>> >> >> > should be at least 6.200000 nm" >>>> >> >> In the past people have ran simulations, where max (in >>>> >> >> settings.xml) >>>> >> >> and rvdw (in grompp.mdp) where not consistent. >>>> >> >> Same for table_end and (rvdw+table-extension). So we have added a >>>> >> >> minimum of consistency checks. >>>> >> >> Of course we cannot check all possible gromacs options and >>>> >> >> combinations. >>>> >> >> e.g. I don't even know if rvdw_switch works with tables at all. >>>> >> >> >>>> >> >> > >>>> >> >> > Would you please advise? Tutorials are supported by older >>>> >> >> > Gromacs >>>> >> >> > versions >>>> >> >> > as none of those settings are in the mdp file. >>>> >> >> All the tutorial should work with gromacs 4.6, I have tested some >>>> >> >> of >>>> >> >> them recently. >>>> >> >> >>>> >> >> But remember, whenever you don't put an option in the mdp file >>>> >> >> gromacs >>>> >> >> will use its internal defaults (see the gromacs manual) and the >>>> >> >> might >>>> >> >> lead to the error here. >>>> >> >> >>>> >> >> I would use: >>>> >> >> rvdw = 1.4 >>>> >> >> table-extension = 2 >>>> >> >> don't see >>>> >> >> rvdw_switch and rlistlong >>>> >> >> >>>> >> >> max = 1.4 >>>> >> >> table_end = 3.4 >>>> >> >> >>>> >> >> You could try to run the spce/ibi tutorial to see if something is >>>> >> >> wrong with your gromacs version. >>>> >> > >>>> >> > >>>> >> > Thank you. I am using 4.5.5. Looking at my distributions (RDF) thy >>>> >> > go >>>> >> > to >>>> >> > zero just before 3 nm. Shall I set then: >>>> >> > >>>> >> > rvdw = 3.0 >>>> >> > table-extension = 4 ; >>>> >> > don't see >>>> >> > rvdw_switch and rlistlong >>>> >> > >>>> >> > max = 3 >>>> >> > table_end = 7 ; = 2*cutoff+1 >>>> >> > >>>> >> > >>>> >> > And my table will be from 0 to 7 then. Would that work? >>>> >> Looks good to me. >>>> > >>>> > >>>> > Getting an error in terms of the extrapolation: >>>> > >>>> > llegal division by zero at >>>> > /apps/votca/1.2.3/share/votca/scripts/inverse/table_extrapolate.pl >>>> > line 227. >>>> > >>>> > ########################################################################################################################################################################################################################################## >>>> > # >>>> > # >>>> > # ERROR: >>>> > # >>>> > # do_external: subscript >>>> > /apps/votca/1.2.3/share/votca/scripts/inverse/table_extrapolate.pl >>>> > --function exponential --avgpoints 5 --region left >>>> > ACI-ACI.pot.smooth.13lKf >>>> > ACI-ACI.pot.extrapol2.tgLGm (from tags table extrapolate) failed # >>>> > # >>>> > # >>>> > >>>> > ########################################################################################################################################################################################################################################## >>>> > >>>> > I tried making tables from csg_stat with maximum value if 3 and 7 and >>>> > the >>>> > same appears. >>>> > >>>> > Any suggestions appreciated. >>>> Have a look at ACI-ACI.pot.smooth.13lKf to see if it looks ok. (Or >>>> post it on the list.) >>>> >>>> > llegal division by zero at >>>> > /apps/votca/1.2.3/share/votca/scripts/inverse/table_extrapolate.pl >>>> > line 227. >>>> line 227 contains: >>>> $grad_beg = ($val[$first + $avgpoints] - $val[$first])/($r[$first + >>>> $avgpoints] - $r[$first]); >>>> it can only be a division by zero error if $r[$first + $avgpoints] >>>> equals $r[$first], which would mean your table is screwed up. >>>> >>>> You might need to increase the min for the ACI-ACI as the >>>> extrapolation on the left fails. >>>> We have made VOTCA a bit smarter about that, but you will need to >>>> install the 1.3-dev version for that. >>>> >>>> > >>>> > Steven >>>> > >>>> > >>>> >> >>>> >> >>>> >> > >>>> >> > Steven >>>> >> >> >>>> >> >> >>>> >> >> >>>> >> >> > >>>> >> >> > >>>> >> >> > Steven >>>> >> >> > >>>> >> >> > >>>> >> >> >> >>>> >> >> >> >>>> >> >> >> > # >>>> >> >> >> > >>>> >> >> >> > I have table.xvg with "zeros" as well as all the files. >>>> >> >> >> > >>>> >> >> >> > Would you pelase advise? >>>> >> >> >> > >>>> >> >> >> > Steven >>>> >> >> >> > >>>> >> >> >> > >>>> >> >> >> > >>>> >> >> >> > >>>> >> >> >> > -- >>>> >> >> >> > 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. >>>> >> >> >> > 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. >>>> >> >> > 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. >>>> >> > 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. >>>> > 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. > 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. 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