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 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.
