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] <javascript:>> 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?
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] <javascript:>) > > 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] <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.
