W dniu poniedziałek, 8 lipca 2013 16:44:20 UTC+1 użytkownik Christoph Junghans napisał: > > 2013/7/8 <s.neu...@gmail.com <javascript:>>: > > > > > > 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? 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 <javascript:>. > > To post to this group, send email to vo...@googlegroups.com<javascript:>. > > > 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.
