Hi Christoph, it seems to work now. The first step is started without any error. I needed the table_bin=0.0005 because I am using the double precision. I know that for a CG it is not really necessary but I need a CG potential for an Adaptive Resolution simulation. I want to thank you again for your time.
Francesca On Dec 28, 2014, at 3:07 PM, Christoph Junghans <[email protected]> wrote: > 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 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.
