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 # 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 votca+unsubscr...@googlegroups.com. To post to this group, send email to votca@googlegroups.com. Visit this group at http://groups.google.com/group/votca. For more options, visit https://groups.google.com/groups/opt_out.