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. >> >> >> > >> >> >> >> > 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. 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