Thank you for your suggestions! I am pretty new with the AdResS so I am still trying different approaches so I really appreciate your suggestions.
Best, Francesca Il 30/dic/2014 18:40 "Christoph Junghans" <[email protected]> ha scritto: > 2014-12-30 3:22 GMT-07:00 Francesca Stanzione < > [email protected]>: > > Hi Christoph, > > it seems to work now. The first step is started without any error. > That is good news. > > > 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. > Remember, that it is enough to interpolate the table to 0.0005, which > VOTCA does automatically for step>table_bin. > One does not need to sample the distributions and calculate the IBI > update for this fine spacing. > > The only good (and common) reason for double precision is energy > conservation, which only is fulfilled by H-AdResS. > For the normal AdResS, which is implement in Gromacs, single > precision is sufficient as the hybrid region needed to be heavily > thermostated. > > In addition, in AdResS the CG region mainly acts as a simplified > system to speedup the simulation, the interesting stuff happens in the > atomistic region, which is covered by the atomistic force field. > Making a too complicated CG model for an AdResS simulation might take > longer than running a brute-force atomistic simulation ;-) > > However, good luck, > > Christoph > > > 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. > > > > -- > 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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