2014-12-19 11:41 GMT-07:00 Francesca Stanzione <[email protected]>: > Thank you Christoph, > I will try the update. About the spacing you are perfectly right I am using > 0.01 and I hope is fine but for the ABB angle spacing 0.00005 was the only > way to don't have "o" values after 170 degree, but I probably with the > update I can use a reasonable space. Yeah, picking min and max for bonded interactions isn't trivial. You want a point where the distribution is non-zero, but where the extrapolation already work.
In your case, I might be easier to fit target distribution with 2 gaussian (e.g. in gnuplot: g1(x)=a*exp(b*(x-c)**2) c=1 g2(x)=d*exp(e*(x-f)**2) f=2.35 fit [0.86:1.15] g1(x) "ABB-angle.dist.tgt" via a,b,c fit [1.15:3.1] g2(x) "ABB-angle.dist.tgt" via d,e,f plot "ABB-angle.dist.tgt", g1(x)+g2(x) ) and Boltzmann invert the outcome by hand and give it to VOTCA as initial guess (ABB-angle.pot.in). Christoph > Thank you again, > Francesca > > Il 19/dic/2014 13:24 "Christoph Junghans" <[email protected]> ha scritto: >> >> 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 -- 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.
