Hi Christoph, unfortunately I tried to update the votca version but it is not working. I have the same error. I changed the spacing in the settings.xml to a reasonable one (0.002) and I also changed the spacing in the ABB-angle.dist.tgt. Any additional suggestion?
Thank you, Francesca 2014-12-19 13:24 GMT-05:00 Christoph Junghans <[email protected]>: > > 2014-12-18 15:36 GMT-07:00 Francesca Stanzione < > [email protected]>: > > Dear all, > > I am experiencing a problem to convert the angle potential in a table.xvg > > I have a polymer chain composed by 7 beads with two beadstypes A and B. > The > > polymer sequence is: A1-B1-B2-B3-B4-B5-A2. I have 2 bondtypes (AB and BB) > > and two angletypes (ABB and BBB). > > I obtained the dist.tgt. When I try to run the IBI it works for the bonds > > but not for the angles. Because I supposed I was doing something wrong I > > tried the hexane and propane tutorials to see if something was wrong > with my > > angles or my settings.xml and I am not able to obtained the tabulated > > potential for angle neither for them. > > This is the error I get: > > ERROR: > > # > > # do_external: subscript > > # > > # /home/software/votca/share/votca/scripts/inverse/table_to_xvg.pl --max > > 1000000 --type angle ABB-angle.pot.shift.YkwA2 table_a0.xvg # > > # (from tags convert_potential xvg) failed > > # > > # For details see the logfile inverse.log > > > > > > THIS IS the DETAILS FROM THE inverse.log > > > > or_all: run 'do_external convert_potential gromacs > > $(csg_get_interaction_property name).pot.cur > $(csg_get_interaction_property > > inverse.gromacs.table)' for interaction named 'ABB-angle' > > Running subscript 'potential_to_gromacs.sh ABB-angle.pot.cur > table_a0.xvg' > > (from tags convert_potential gromacs) dir > > /home/software/votca/share/votca/scripts/inverse > > Convert ABB-angle.pot.cur to table_a0.xvg > > Running critical command 'sed -n s/.*cg_bonded\.\([^[:space:]]*\) > .*/\1/p' > > Running critical command 'mktemp ABB-angle.pot.scale.XXXXX' > > Running subscript 'table_linearop.pl --on-x ABB-angle.pot.cur > > ABB-angle.pot.scale.dHEeQ 57.2957795 0' (from tags table linearop) dir > > /home/software/votca/share/votca/scripts/inverse > > table_linearop.pl: ABB-angle.pot.cur to ABB-angle.pot.scale.dHEeQ with > x' = > > 57.2957795*x + 0 > > Running critical command 'mktemp ABB-angle.pot.smooth.XXXXX' > > Running critical command 'csg_resample --in ABB-angle.pot.scale.dHEeQ > --out > > ABB-angle.pot.smooth.bZWVq --grid 0:0.0286479:180' > > Running critical command 'mktemp ABB-angle.pot.extrapol.XXXXX' > > Running subscript 'potential_extrapolate.sh --type angle > > ABB-angle.pot.smooth.bZWVq ABB-angle.pot.extrapol.3ThKw' (from tags > > potential extrapolate) dir > /home/software/votca/share/votca/scripts/inverse > > Extrapolate ABB-angle.pot.smooth.bZWVq to ABB-angle.pot.extrapol.3ThKw > > Running subscript 'table_extrapolate.pl --function linear --avgpoints 3 > > --region leftright ABB-angle.pot.smooth.bZWVq > ABB-angle.pot.extrapol.3ThKw' > > (from tags table extrapolate) dir > > /home/software/votca/share/votca/scripts/inverse > > table_extrapolate.pl: extrapolating the left using linear with gradient > > -8.60697674418617 > > table_extrapolate.pl: extrapolating the right using linear with gradient > > -0.0167414651162821 > > Running critical command 'mktemp ABB-angle.pot.interpol.XXXXX' > > Running critical command 'csg_resample --in ABB-angle.pot.extrapol.3ThKw > > --out ABB-angle.pot.interpol.j2iBK --grid 0:0.0005:180 --comment Created > on > > Thu Dec 18 16:38:36 EST 2014 by fstanzio@silicon > > called from potential_to_gromacs.sh, version 1.3-dev hgid: 4fce95a62b88 > > settings file: > /home/Documents/bigger_box/reaction/ibi_cou_user/settings.xml > > working directory: > /home/Documents/bigger_box/reaction/ibi_cou_user/step_001 > > Comments from > > > /home/Documents/bigger_box/reaction/ibi_cou_user/step_001/ABB-angle.pot.cur:\nCreated > > on Thu Dec 18 16:38:30 EST 2014 by fstanzio@silicon > > called from prepare_generic_single.sh, version 1.3-dev hgid: 4fce95a62b88 > > settings file: > /home/Documents/bigger_box/reaction/ibi_cou_user/settings.xml > > working directory: > > /home/Documents/bigger_box/reaction/ibi_cou_user/step_000' > > Running critical command 'mktemp ABB-angle.pot.shift.XXXXX' > > Running subscript 'potential_shift.pl --type angle > > ABB-angle.pot.interpol.j2iBK ABB-angle.pot.shift.YkwA2' (from tags > potential > > shift) dir /home/software/votca/share/votca/scripts/inverse > > Running subscript 'table_to_xvg.pl --max 1000000 --type angle > > ABB-angle.pot.shift.YkwA2 table_a0.xvg' (from tags convert_potential xvg) > > dir /home/software/votca/share/votca/scripts/inverse > > Illegal division by zero at > > /home/fstanzio/software/votca/share/votca/scripts/inverse/ > table_to_xvg.pl > > line 96. > > > > Checking the xxx.pot.shift file I have "o" on the last 5 values, I tried > to > > resample, to change the --grid to 179.5 (last value with "i") but > nothing is > > working.. > > > > I have the version 1.3-dev. > > > > I am sending you in addition the ABB-angle.dist.tgt and the settings.xml > > files. > > Can you please help me to understand what is the problem and why I am not > > able to have a table_angle? > Ok, it looks like ABB-angle.dist.tgt gets converted to > ABB-angle.pot.cur in step_000 and the conversion from > ABB-angle.pot.cur to > table_a0.xvg. > > However, with the latest version of VOTCA 1.3-dev (changeset: > 1e124eb53c82) I wasn't able to reproduce this problem, so please as > 0th step re-install VOTCA and see if the problem persists. > (<https://code.google.com/p/votca/wiki/Installing#Development_Version>) > > Independently, after looking at your files, I have a couple of issues: > 1.) a spacing of 0.02 in ABB-angle.dist.tgt might be a bit to fine, > when looking at the curve around 2.35, it very rough. IBI will never > be able to fit that. You will have to smooth the target distribution > first. > 2.) a spacing of 0.0005 for ABB-angle in settings.xml is by far too > fine. You will have to run really really long cg simulation in each > iteration to fill the 4400 (=2.2/0.0005) bins of that interaction with > statistic. > Remember that the stepping for each interaction doesn't have to be the > same as table_bins in gromacs block. > > Cheers, > > Christoph > > > > > > > > > Thank you, > > Francesca > > > > -- > > 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/d/optout. > > > > -- > Christoph Junghans > Web: http://www.compphys.de > > -- > You received this message because you are subscribed to a topic in the > Google Groups "votca" group. > To unsubscribe from this topic, visit > https://groups.google.com/d/topic/votca/wcSWx0n900s/unsubscribe. > To unsubscribe from this group and all its topics, 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/d/optout. > -- You received this message because you are subscribed to the Google Groups "votca" group. 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