2013/7/8 <s.neuman...@gmail.com>: > 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.
> # > > 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. > > -- 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 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.
