2013/7/10 <[email protected]>: > > > On Wednesday, July 10, 2013 7:00:16 PM UTC+1, [email protected] wrote: >> >> Thank you. I sorted it out. >> Sorry, I have another question: I am running IBI on the cluster so I >> specified in my PBS script 16 cpus. When I run gromacs I always add mpiexec >> before mdrun. I run votca with mpiexec before executing IBI. The job is >> running and inverse.log stopped on: >> >> :-) grompp (-: >> >> This run will generate roughly 17 Mb of data >> run_gromacs.sh: No walltime defined, so no time limitation given to mdrun >> Running critical command 'mdrun -s topol.tpr -c confout.gro -o traj.trr -x >> traj.xtc >> >> Cannot see any files traj.xtc etc. in my 001 step. Would you advise >> please? You could set cg.inverse.gromacs.mdrun.command to "mpiexec mdrun" in your xml file.
> > > > I run it manually and it works, however after the 1st step when finishing > the gromacs run: > > Running critical command 'csg_stat --nt 32 --options > /work/jkm210/COARSE_GRAINED/CHANDLER/IBI_NON2/settings.xml --top topol.tpr > --trj traj.xtc --begin 10 --first-frame 0' > begin to calculate distribution functions > # of bonded interactions: 0 > # of non-bonded interactions: 15 > an error occurred: > input format not supported: topol.tpr > > Which means my votca is not fully compiled with Gromacs. I cannot change > anything in both Votca or Gromacs as I am not an admin on the clsuter. Can I > manually compile it somehow? See: <https://code.google.com/p/votca/wiki/Installing#From_Source> "csg_stat --help" should show the gromacs version it is compiled with in the top somewhere. > > Steven > >> >> >> On Wednesday, July 10, 2013 4:16:10 PM UTC+1, Christoph Junghans wrote: >>> >>> 2013/7/10 <[email protected]>: >>> > 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 [email protected] >>> > 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 <[email protected]>: >>> >> > 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, [email protected] >>> >> > 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 <[email protected]>: >>> >> >>> > >>> >> >>> > >>> >> >>> > W dniu poniedziałek, 8 lipca 2013 18:00:32 UTC+1 użytkownik >>> >> >>> > Christoph >>> >> >>> > Junghans napisał: >>> >> >>> >> >>> >> >>> >> 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. >>> >> >>> > >>> >> >>> > >>> >> >>> > 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 [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. >>> >> >>> > >>> >> >>> > >>> >> >>> >>> >> >>> >>> >> >>> >>> >> >>> -- >>> >> >>> 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. > > -- Christoph Junghans 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