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. > 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)
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 the Google Groups "votca" group. 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