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. > > 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 <http://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' 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/inver > se/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/to > pic/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.
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BI-bond-H1-L.pot.ib
Description: Binary data
<cg>
<bonded>
<name>bond-H1-L</name>
<min>0.3425</min>
<max>0.348</max>
<step>0.0005</step>
</bonded>
<inverse>
<gromacs>
<pot_max>1e8</pot_max>
<table_end>1.0</table_end>
<table_bins>0.0001</table_bins>
</gromacs>
</inverse>
</cg>
Harmonic-bond-H1-L.pot.ib
Description: Binary data
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