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.
> > 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.
