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. > > > 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.
