2013/7/8 <s.neuman...@gmail.com>: > > > W dniu poniedziałek, 8 lipca 2013 18:00:32 UTC+1 użytkownik Christoph > Junghans napisał: >> >> 2013/7/8 <s.neu...@gmail.com>: >> > >> > >> > W dniu poniedziałek, 8 lipca 2013 16:44:20 UTC+1 użytkownik Christoph >> > Junghans napisał: >> >> >> >> 2013/7/8 <s.neu...@gmail.com>: >> >> > >> >> > >> >> > W dniu poniedziałek, 8 lipca 2013 14:39:49 UTC+1 użytkownik Christoph >> >> > Junghans napisał: >> >> >> >> >> >> 2013/7/8 <s.neu...@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. >> >> > >> >> > >> >> > 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 votca+un...@googlegroups.com. >> >> >> > To post to this group, send email to vo...@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+un...@googlegroups.com. >> >> > To post to this group, send email to vo...@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+un...@googlegroups.com. >> > To post to this group, send email to vo...@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. > > -- 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.
