On Sat, May 5, 2018 at 5:46 AM, Alexander Alexander <[email protected]> wrote: > Hi Christoph, > > Any idea, please? I am out of ideas for now!
> > > On Thursday, May 3, 2018 at 5:50:15 PM UTC-4, Alexander Alexander wrote: >> >> >> >> On Thursday, May 3, 2018 at 4:56:25 PM UTC-4, Christoph Junghans wrote: >>> >>> On Thu, May 3, 2018 at 1:46 PM, Alex <[email protected]> wrote: >>> > >>> > 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. >>> Ok, I think there is some confusion about table format. >>> >>> The Gromacs (xvg) table format is: >>> first column : Distance with unit nm >>> Second column : Energy with unit KJ/mol >>> Thirst column: Force with unit KJ/mol/nm >>> >>> However the VOTCA table format is just >>> first column : Distance in simulation backend units >>> Second column : Energy in simulation backend units >>> Third column: flag >>> (see section 3.6 of the VOTCA manual) >> >> Probably you mena the *.pot.ib or *.pot.in we get from csg_boltzmann. >> Otherwise after converting them to the gromacs format by by csg_call... .. >> convert_potential gromacs... they have the gromacs units and formats. >>> >>> >>> >> > 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 >>> > 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' >>> Looking at Harmonic-bond-H1-L.pot.ib, something is screwed up. >>> You have duplicated r values. >>> $ head Harmonic-bond-H1-L.pot.ib >>> 0.3432 0.002205 2.1 >>> 0.3432 0.002205 2.1 >>> >>> Something like: >>> $ awk 'BEGIN{for(r=0.3425;r<0.3481;r+=0.0005){print >>> r,((r-0.34530000)**2)*(1000/2)},"i";}' > Harmonic-bond-H1-L.pot.ib >>> $ csg_call --ia-type bond --ia-name bond-H1-L --options bond-H1-L.xml >>> convert_potential gromacs Harmonic-bond-H1-L.pot.ib table_b2.xvg >>> should work! >> >> Wow, it works now, thank you. >> Just one issue; in "2 3 2 0.3453 K" of harmonic potential , different >> K from 500 to 50000 could work in this system, and then each K would give >> different pot.ib and table_b2.xvg of course with >> (r-0.34530000)**2)*(1000/2), so, which one (K) is good to choose? > > Additionally, why using the "2 3 2 0.3453 K" in the harmonic format > works fine in a calculation, but it does not work soemtimes when I convert > the "0.3453 K" to the table format following the remedy above? Have another look here: http://www.gromacs.org/Documentation/How-tos/Tabulated_Potentials#Constructing_the_Table(s) If you are doing the table right, otherwise this sounds like a bug in gromacs to me! Christoph >> >> >> One more question: >> After a IBI-nonbonded for a system, I am doing now IBI-bonded-nonbonded >> for that system which has two bond types and one angle. They started with a >> promising fit with their dist.tgt's but afterward they do not have any >> sensible improvement after 115 step now, even the angle.dist.new is loosing >> gradually its agreement with angle.dist.tgt. I was wondering what might be >> the reason? Below is part of my settings.xml file: The <scale>1.5</scale> in >> the first bond I choose just because I though it might help improvement, but >> no considerable improvement. >> >> <name>bond-D-E</name> >> <min>0.200</min> >> <max>0.500</max> >> <step>0.0005</step> >> <inverse> >> <target>bond-D-E.dist.tgt</target> >> <do_potential>1 0 0</do_potential> >> <post_update>smooth</post_update> >> <post_update_options> >> <scale>1.5</scale> >> </post_update_options> >> <post_add>convergence</post_add> >> <gromacs> >> <table>table_b1.xvg</table> >> </gromacs> >> </inverse> >> </bonded> >> <!-- %%% --> >> <bonded> >> <name>angle-D-E-F</name> >> <min>2.0</min> >> <max>3.0</max> >> <step>0.001</step> >> <inverse> >> <target>angle-D-E-F.dist.tgt</target> >> <do_potential>0 0 1</do_potential> >> <post_update>smooth</post_update> >> <post_update_options> >> <scale>0.1</scale> >> </post_update_options> >> <post_add>convergence</post_add> >> <gromacs> >> <table>table_a1.xvg</table> >> </gromacs> >> </inverse> >> </bonded> > > > Best regards, > Alex >> >> >> Thank you. >> Regards, >> Alex >>> >>> >>> Christoph >>> >>> >>> > >>> > 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/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 a topic in the >>> >> Google Groups "votca" group. >>> >> To unsubscribe from this topic, visit >>> >> https://groups.google.com/d/topic/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. >>> >>> >>> >>> -- >>> 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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