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] <javascript:>> 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?
> > > > >> > >> > 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 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] <javascript:>. > > To post to this group, send email to [email protected] > <javascript:>. > > 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.
