Hi Christoph, Any idea, please?
On Thursday, May 3, 2018 at 5:50:15 PM UTC-4, Alexander Alexander wrote: > > > > On Thursday, May 3, 2018 at 4:56:25 PM UTC-4, Christoph Junghans wrote: >> >> On Thu, May 3, 2018 at 1:46 PM, Alex <[email protected]> wrote: >> > >> > On Thu, May 3, 2018 at 3:03 PM, Christoph Junghans <[email protected]> >> > wrote: >> >> >> >> On Thu, May 3, 2018 at 12:44 PM, Alexander Alexander >> >> <[email protected]> wrote: >> >> > Hi Christoph, >> >> > >> >> > On Wednesday, May 2, 2018 at 9:29:51 PM UTC-4, Christoph Junghans >> wrote: >> >> >> >> >> >> On Wed, May 2, 2018 at 4:37 PM, Alexander Alexander >> >> >> <[email protected]> wrote: >> >> >> > Thanks. >> >> >> > >> >> >> > On Wednesday, May 2, 2018 at 5:54:50 PM UTC-4, Christoph Junghans >> >> >> > wrote: >> >> >> >> >> >> >> >> On Wed, May 2, 2018 at 3:37 PM, Alexander Alexander >> >> >> >> <[email protected]> wrote: >> >> >> >> > Hi Christoph, >> >> >> >> > Thanks. >> >> >> >> > >> >> >> >> > On Wednesday, May 2, 2018 at 5:13:13 PM UTC-4, Christoph >> Junghans >> >> >> >> > wrote: >> >> >> >> >> >> >> >> >> >> On Wed, May 2, 2018 at 1:38 PM, Alexander Alexander >> >> >> >> >> <[email protected]> wrote: >> >> >> >> >> > Dear all, >> >> >> >> >> > I did a >> >> >> >> >> > My IBI-bonded-nonbonded (after getting the nonbonded >> potentials >> >> >> >> >> > via >> >> >> >> >> > IBI-nonbonded only) crashes dues to the "...bonded >> interactions >> >> >> >> >> > could >> >> >> >> >> > not be >> >> >> >> >> > calculated because some atoms >> >> >> >> >> > involved moved further apart ...". By replacing the >> ill-bond by >> >> >> >> >> > a >> >> >> >> >> > harmonic >> >> >> >> >> > potential in topol.top file "2 3 N 0.3453 K" where N = >> 1,2 >> >> >> >> >> > and >> >> >> >> >> > K >> >> >> >> >> > = >> >> >> >> >> > 5000, >> >> >> >> >> > the simulation are going well. Now what? what is the >> relation >> >> >> >> >> > between >> >> >> >> >> > this >> >> >> >> >> > harmonic and the table_b2.xvg which was replaced by the >> >> >> >> >> > harmonic >> >> >> >> >> > one? >> >> >> >> >> > What >> >> >> >> >> > would happen for the table_b2.xvg? >> >> >> >> >> Sorry, I don't understand your question! Can you rephrase? >> >> >> >> >> >> >> >> >> > Let's say the calculation crashes when table_b2.xvg is used >> but it >> >> >> >> > works >> >> >> >> > fine with "2 3 2 0.3453 1000" instead, then my question is >> >> >> >> > that >> >> >> >> > "should >> >> >> >> > I continue the preregistration using "2 3 2 0.3453 1000" >> and >> >> >> >> > forget >> >> >> >> > about the table_b2.xvg? If so, what would be the final right >> >> >> >> > table_b2.xvg at >> >> >> >> > the end? If not so, how I can take benefit from the knowledge >> of >> >> >> >> > "2 >> >> >> >> > 3 >> >> >> >> > 2 >> >> >> >> > 0.3453 1000" to improve the table_b2.xvg so that it would >> work as >> >> >> >> > well? >> >> >> >> You know generate a table with k*(r-r_0) (with r_0=0.3453 >> andk=1000, >> >> >> >> clip out the middle part and replace it with the structured part >> >> >> >> from >> >> >> >> BI. >> >> >> >> >> >> >> >> >> >> > OK, I see. >> >> >> > How about this instead: >> >> >> > The reason that the calculation crashes with table_b2.xvg is that >> the >> >> >> > table_b2.xvg represents a very low K (spring constant) so that >> the >> >> >> > two >> >> >> > atoms >> >> >> > are getting apart. I was reading somewhere in the mailing list >> that >> >> >> > the >> >> >> > last >> >> >> > number in "2 3 8 2 1 ; 1:bond-H1-L:1" is a kind of factor >> for >> >> >> > the >> >> >> > third >> >> >> > column of the table_b2.xvg, so, don't you think it would be >> possible >> >> >> > to >> >> >> > increase this factor to 2 or 3 (which means multiplying the third >> >> >> > column) >> >> >> > until the calculation goes fine? >> >> >> Yeah, that sounds reasonable! Increasing the K helps usually helps >> >> >> with the atoms getting too far apart. >> >> >> >> >> >> If you want to scale column 3 you will also have to modify column 2 >> >> >> accordingly. >> >> >> Gromacs won't allow mismatching columns. >> >> > >> >> > I tried to scale both of the column 2 and 3 of table_b2.xvg using a >> lot >> >> > of >> >> > scale-factor, but they did not work and the missing bond ... error >> is >> >> > still >> >> > here., I guess finding the right factor is not easy. >> >> > So, I tried your suggestion above, I mean k*(r-r_0) (with r_0=0.3453 >> >> > andk=1000. T do so, I first created a bond.pot.ib potential >> including 3 >> >> > columns as following: >> >> > #----------------- >> >> > bond.pot.in >> >> > #column1 #column2 # column3 >> >> > r (1000/2)*(r-0.3453)^2 -(1000)*(r-0.3453) >> >> > #------------------- >> >> > And added the letter "i" to the end of each row. >> Ok, I think there is some confusion about table format. >> >> The Gromacs (xvg) table format is: >> first column : Distance with unit nm >> Second column : Energy with unit KJ/mol >> Thirst column: Force with unit KJ/mol/nm >> >> However the VOTCA table format is just >> first column : Distance in simulation backend units >> Second column : Energy in simulation backend units >> Third column: flag >> (see section 3.6 of the VOTCA manual) >> > Probably you mena the *.pot.ib or *.pot.in we get from csg_boltzmann. > Otherwise after converting them to the gromacs format by by csg_call... .. > convert_potential gromacs... they have the gromacs units and formats. > >> >> >> > Then I tried to converted the above bond.pot.in to table_b2.xvg >> using >> >> > "csg_call --ia-type bond --ia-name bond-H1-L --options bond-H1-L.xml >> >> > convert_potential gromacs ...". But then all of the second and third >> >> > columns >> >> > of the new table_b2.xvg was just nan -nan. >> >> > Would you please let me know if the procedure is right and where I >> am >> >> > doing >> >> > wrong? >> >> Not sure, can you post your input files? (pot.in and xml) >> > >> > Thanks. >> > Please find attached the files pot.in = Harmonic-bond-H1-L.pot.in >> > The two other files are the potential associated with this bond >> obtained by >> > normal BI crashing the calculation. >> > I simply calculate the harmonic files using these two awk command: >> > >> > awk -v CONVFMT=%.7g '{$3 = (($1 - 0.34530000)**2)*(1000/2)} 1' >> > awk -v CONVFMT=%.7g '{$4 = ($1 - 0.34530000)*(-1000)} 1' >> Looking at Harmonic-bond-H1-L.pot.ib, something is screwed up. >> You have duplicated r values. >> $ head Harmonic-bond-H1-L.pot.ib >> 0.3432 0.002205 2.1 >> 0.3432 0.002205 2.1 >> >> Something like: >> $ awk 'BEGIN{for(r=0.3425;r<0.3481;r+=0.0005){print >> r,((r-0.34530000)**2)*(1000/2)},"i";}' > Harmonic-bond-H1-L.pot.ib >> $ csg_call --ia-type bond --ia-name bond-H1-L --options bond-H1-L.xml >> convert_potential gromacs Harmonic-bond-H1-L.pot.ib table_b2.xvg >> should work! >> > Wow, it works now, thank you. > Just one issue; in "2 3 2 0.3453 K" of harmonic potential , different > K from 500 to 50000 could work in this system, and then each K would give > different pot.ib and table_b2.xvg of course with > (r-0.34530000)**2)*(1000/2), so, which one (K) is good to choose? > Additionally, why using the "2 3 2 0.3453 K" in the harmonic format works fine in a calculation, but it does not work soemtimes when I convert the "0.3453 K" to the table format following the remedy above? > > One more question: > After a IBI-nonbonded for a system, I am doing now IBI-bonded-nonbonded > for that system which has two bond types and one angle. They started with a > promising fit with their dist.tgt's but afterward they do not have any > sensible improvement after 115 step now, even the angle.dist.new is loosing > gradually its agreement with angle.dist.tgt. I was wondering what might be > the reason? Below is part of my settings.xml file: The <scale>1.5</scale> > in the first bond I choose just because I though it might help improvement, > but no considerable improvement. > > <name>bond-D-E</name> > <min>0.200</min> > <max>0.500</max> > <step>0.0005</step> > <inverse> > <target>bond-D-E.dist.tgt</target> > <do_potential>1 0 0</do_potential> > <post_update>smooth</post_update> > <post_update_options> > <scale>1.5</scale> > </post_update_options> > <post_add>convergence</post_add> > <gromacs> > <table>table_b1.xvg</table> > </gromacs> > </inverse> > </bonded> > <!-- %%% --> > <bonded> > <name>angle-D-E-F</name> > <min>2.0</min> > <max>3.0</max> > <step>0.001</step> > <inverse> > <target>angle-D-E-F.dist.tgt</target> > <do_potential>0 0 1</do_potential> > <post_update>smooth</post_update> > <post_update_options> > <scale>0.1</scale> > </post_update_options> > <post_add>convergence</post_add> > <gromacs> > <table>table_a1.xvg</table> > </gromacs> > </inverse> > </bonded> > Best regards, Alex > > Thank you. > Regards, > Alex > >> >> Christoph >> >> >> > >> > Regards, >> > Alex >> > >> >> >> >> Christoph >> >> > >> >> > Thank you. >> >> > Alex >> >> > >> >> >> >> >> >> >> >> >> >> >> >> > >> >> >> >> >> >> >> >> >> >> > Figures in attachment are the plot of >> >> >> >> >> > table_b2.xvg. >> >> >> >> >> > I got the bonded tables including the table_b2.xvg by >> >> >> >> >> > "csg_boltzmann" >> >> >> >> >> > --> >> >> >> >> >> > "csg_call --sloppy-tables" ---> "csg_call --ia-type bond >> >> >> >> >> > --ia-name >> >> >> >> >> > bond >> >> >> >> >> > ... >> >> >> >> >> > gromacs table_b2.xvg". And I am using the bond(angle)-*. >> pot.in >> >> >> >> >> > as >> >> >> >> >> > initial >> >> >> >> >> > guesses for my IBI-all. >> >> >> >> >> > >> >> >> >> >> > The table_b1.xvg in gromacs manual has been defined such >> that >> >> >> >> >> > the >> >> >> >> >> > the >> >> >> >> >> > r(nm), >> >> >> >> >> > f(r), f'(r) are the first, second and third column of >> >> >> >> >> > table_b2.xvg >> >> >> >> >> > where >> >> >> >> >> > f(r) is a cubic spline function in V_b(r_ij) = k*f(r_ij), >> If >> >> >> >> >> > the >> >> >> >> >> > same >> >> >> >> >> > definition is applied for the table_b2.xvg obtained by the >> >> >> >> >> > above >> >> >> >> >> > method? >> >> >> >> >> To be clear, the gromacs table format is x, f(x), -f'(x) (see >> >> >> >> >> gromacs >> >> >> >> >> manual 4.2.14) >> >> >> >> >> >> >> >> >> >> I am not sure what your question is! Gromacs uses cubic >> spline >> >> >> >> >> internal to interpolate the table. >> >> >> >> >> However, if you set cg.inverse.gromacs.table_bins in your xml >> >> >> >> >> file >> >> >> >> >> small enough (you had something like 0.002), then there isn't >> >> >> >> >> much >> >> >> >> >> to >> >> >> >> >> interpolate. >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> > What is the unit of f(r)? >> >> >> >> >> KJ/mol (gromacs energy units) >> >> >> >> >> >> >> >> >> >> > What is the unit of each column in table_b2.xvg in VOTCA? >> >> >> >> >> KJ/mol/nm (gromacs force units) >> >> >> >> > >> >> >> >> > Just to sum up the table format, can you please confirm me >> that >> >> >> >> > the >> >> >> >> > table_b.xvg in VOTCA has the following format: >> >> >> >> > first column : Distance with unit nm >> >> >> >> > Second column : Energy with unit KJ/mol >> >> >> >> > Thirst column: Force with unit KJ/mol/nm >> >> >> >> For bonds (not angles) in gromacs that is the format! >> >> >> > >> >> >> > For angle the first column is degree probably. >> >> >> >> >> >> >> >> >> >> >> >> Also for a different simulation backend, e.g. lammps this will >> be >> >> >> >> different of course, too! >> >> >> > >> >> >> > >> >> >> > I have one more question which your comment on would be highly >> >> >> > appreciated: >> >> >> > In another IBI-bonded-nonbonded parameterization the "mpirun -np >> 64 >> >> >> > gmx_mpi >> >> >> > mdrun" work fine till step_021 of parameterization where it >> crashes >> >> >> > because >> >> >> > it can not find any domain decomposition for 64 ranks that is >> >> >> > compatible >> >> >> > with the system size. Even it works in the minimization >> simulation in >> >> >> > step_021. >> >> >> > I have already read most of the discussions about the error of >> domain >> >> >> > decomposition, and I have tried different options like using >> >> >> > different >> >> >> > ranks >> >> >> > (64, 32, 16, 8, 40, 36) and also -rdd ... or -dds. However, no >> >> >> > success >> >> >> > yet. >> >> >> > I am totally confused with these parameters and I can not solve >> the >> >> >> > issue. >> >> >> > So, below I have shared the md.log files for the step_20 (which >> works >> >> >> > fine) >> >> >> > and step_21 (minimization which works fine) and step_21 (which >> >> >> > crashes), >> >> >> > and >> >> >> > I would be so appreciated if one could help me overcome the >> issue. >> >> >> > About the machine: Running on 4 nodes with total 64 cores, 64 >> logical >> >> >> > cores, >> >> >> > Cores per node: 16. >> >> >> > >> >> >> > md.log-20 >> >> >> > >> https://drive.google.com/open?id=1ZwYggDI1Hy_eYY8_nT8I50t91Wla0Obr >> >> >> > >> >> >> > md.log-21-mini >> >> >> > >> https://drive.google.com/open?id=1oYE4A6fC1L8u_vx4sR8RIq3EWiG9-7YB >> >> >> > >> >> >> > md.log-21 >> >> >> > >> https://drive.google.com/open?id=1ff_QJrdGvLFgwGU9xMY-IcqfxzF2jkAO >> >> >> Sorry, that really is a question for the gromacs user mailing list. >> >> >> ([email protected]) >> >> >> >> >> >> Christoph >> >> >> >> >> >> > >> >> >> > >> >> >> > Thank you very much. >> >> >> > Regards, >> >> >> > Alex >> >> >> >> >> >> >> >> >> >> >> >> Christoph >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> > >> >> >> >> >> > And would you please explain table_b2-1-3.png figure? >> >> >> >> >> Not sure what there is to explain..the code on how the third >> >> >> >> >> column >> >> >> >> >> is >> >> >> >> >> calculated is here: >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> https://github.com/votca/csg/blob/master/share/scripts/inverse/table_to_xvg.pl#L95 >> >> >> >> >> > >> >> >> >> > Best regards, >> >> >> >> > Alex >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> Christoph >> >> >> >> >> >> >> >> >> >> > Thank you very much. >> >> >> >> >> > Regards, >> >> >> >> >> > Alex >> >> >> >> >> > >> >> >> >> >> > -- >> >> >> >> >> > 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 https://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 https://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 https://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 https://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/7Hh-gxZEpmI/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 https://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 https://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. 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