2014-12-28 12:10 GMT-07:00 Christoph Junghans <[email protected]>: > Hi, > > 2014-12-28 4:17 GMT-07:00 Francesca Stanzione <[email protected]>: >> 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? > Ok, I looked at the original problem again and there seems to be a > rounding problem with step/gromacs.table_bins=0.0005. > Basically numbers get rounded in each potential conversion step and > hence after a while one gets the "Illegal division by zero" as two x > values become too similar. I still have not found out, where exactly > it goes wrong and add a warning. I fixed the original issue: <https://code.google.com/p/votca/source/detail?r=cc6ea63f95532302c3d97159b6175b6899266bc7&repo=tools>
Please re-build tools and csg to get it. > > In addition, Gromacs internally uses a spacing of 0.002 (single > precision) or 0.0005 (double precision), so 0.0005 would only make > sense with double precision Gromacs. But double precision isn't really > needed for coarse-grained simulation with thermostats. Have you tried > using gromacs.table_bins=0.002 ? > > With gromacs.table_bins=0.002 and the following patch, I got your > table running in hexane/ibi_bonded example. > diff -r a4ed014029f5 hexane/ibi_bonded/settings.xml > --- a/hexane/ibi_bonded/settings.xml Fri Oct 10 03:40:35 2014 -0600 > +++ b/hexane/ibi_bonded/settings.xml Sun Dec 28 11:54:25 2014 -0700 > @@ -16,12 +16,12 @@ > <bonded> > <!-- name of the interaction --> > <name>angle</name> > - <min>1.7</min> > + <min>0.9</min> > <max>3.1</max> > - <step>0.02</step> > + <step>0.002</step> > <inverse> > <!-- target distribution --> > - <target>angle.dist.tgt</target> > + <target>ABB-angle.dist.tgt</target> > <gromacs> > <table>table_a1.xvg</table> > </gromacs> > > But anyhow, step=0.002 is still 1100 bins which need to be filling > with statistics, which is a lot, you should aim for something like > 0.02. > Like I said in my last email, you might have better chances generating > a custom initial guess for your angle potential. > > Christoph > >> >> 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. >> 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 -- 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.
