2013/7/10 <s.neuman...@gmail.com>: > I run the command to create the file ACI-ACI.in and I got the zero potential > again. The same for two other files... Can you try for me running this > command with my settings.xml please? Attached. below the command and the > outcome > > csg_call --ia-type non-bonded --options settings.xml --ia-name ACI-ACI > prepare_single ibi ACI-ACI.pot.in I think used max=2 yesterday, that's why it worked. With max=3 it won't work as that is exactly what csg_inverse calls internally.
Like I said in the other email, have another thought on how the interactions should look for large r. If is will look bond-like you will have create it yourself (by hand). VOTCA can only support it you with its scripts, but not with any automation. > > Running subscript 'table_extrapolate.pl --function constant --avgpoints 1 > --regi on leftright ACI-ACI.dist.tgt_smooth.19358 > ACI-ACI.dist.tgt'(from tags table ext rapolate) > Running critical command 'mktemp ACI-ACI.pot.new.raw.XXX' > Running subscript 'RDF_to_POT.pl ACI-ACI.dist.tgt > ACI-ACI.pot.new.raw.371'(from tags rdf pot) > Use of uninitialized value in subtraction (-) at > /usr/local/votca/votca-csg-1.2. > 3/share/votca/scripts/inverse/RDF_to_POT.pl line 96. > Use of uninitialized value in subtraction (-) at > /usr/local/votca/votca-csg-1.2. > 3/share/votca/scripts/inverse/RDF_to_POT.pl line 96. > > Use of uninitialized value in addition (+) at > /usr/local/votca/votca-csg-1.2.3/s > hare/votca/scripts/inverse/RDF_to_POT.pl line 99. > Running critical command 'mktemp ACI-ACI.pot.new.smooth.XXX' > Running critical command 'csg_resample --in ACI-ACI.pot.new.raw.371 --out > ACI-AC I.pot.new.smooth.385 --grid 0:0.01:3 --comment Created on > Wed Jul 10 16:00:27 BS T 2013 by jkm...@psl119.ps.ic.ac.uk > called from prepare_generic_single.sh, version 1.2.3 > settings file: > /home/ps/ps-fs2/jkm210/Polyglycine/CHANDLER/IBI_NON/Dist2Pot/sett > ings.xml > working directory: > /home/ps/ps-fs2/jkm210/Polyglycine/CHANDLER/IBI_NON/Dist2Pot' > Running subscript 'dpot_shift_nb.pl ACI-ACI.pot.new.smooth.385 > ACI-ACI.pot.new'( from tags pot shift_nonbonded) > > > > W dniu wtorek, 9 lipca 2013 16:15:08 UTC+1 użytkownik Christoph Junghans > napisał: >> >> 2013/7/9 <s.neu...@gmail.com>: >> > This is what fails and produces the zero potential: >> > >> > Running subscript 'RDF_to_POT.pl ACI-ACI.dist.tgt >> > ACI-ACI.pot.new.raw.396'(from tags rdf pot) >> > Use of uninitialized value in subtraction (-) at >> > >> > /usr/local/votca/votca-csg-1.2.3/share/votca/scripts/inverse/RDF_to_POT.pl >> > line 96. >> > Use of uninitialized value in subtraction (-) at >> > >> > /usr/local/votca/votca-csg-1.2.3/share/votca/scripts/inverse/RDF_to_POT.pl >> > line 96. >> > Use of uninitialized value in addition (+) at >> > >> > /usr/local/votca/votca-csg-1.2.3/share/votca/scripts/inverse/RDF_to_POT.pl >> > line 99. >> > >> > Would you advise please? >> Please send your ACI-ACI.dist.tgt. Was it generated from the ACI-ACI >> rdf you send before? >> >> > >> > >> > On Tuesday, July 9, 2013 10:04:55 AM UTC+1, s.neu...@gmail.com wrote: >> >> >> >> I tried increasing min, changed the maximum of potential and it still >> >> provides me with zero potentials... I cannot upgrade to 1.3 as I am not >> >> an >> >> administrator. >> >> >> >> On Monday, July 8, 2013 10:26:41 PM UTC+1, Christoph Junghans wrote: >> >>> >> >>> 2013/7/8 <s.neu...@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+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. 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