On Thu, Apr 11, 2019 at 1:26 PM Aditi Khot <[email protected]> wrote: > > Thank you. The hybrid methods paper was very helpful. Also, one more question: > While setting up the system of equations, do the forces on a CG bead exclude > all the intramolecular non-bonded forces at the CG level? I am not talking > about the target or reference forces, but the inputs which form the 'A > matrix' of the linear system. In case of polymers, we may want to include CG > interactions within a molecules beyond 1-4 interaction. > You can simply check the exclusions VOTCA is using by running: $ csg_dump --top topology.xml --cg mapping.xml --excl
Christoph > Thanks, > Aditi. > > > > On Thu, Apr 11, 2019 at 12:33 PM Christoph Junghans <[email protected]> > wrote: >> >> On Thu, Apr 11, 2019 at 9:39 AM Aditi Khot <[email protected]> wrote: >> > >> > Thank you. I wasn't using the correct sampling range. >> > >> > I had a few more questions: >> > 1. How is the force matching error reported? >> > What does the error column mean? Is it the variance of force value over >> > different blocks at that radial distance? >> If I recall correctly this is the block error for the different blocks. >> >> > 2. What does the output 'This should be a number:' mean? >> This is just a check if the spline calculation was successful, i.e. >> the spline coefficient should be a number. >> We might need to improve this error message... >> >> > 3. Is the constraint for virial/ pressure matching implemented in votca? >> No, but patches are welcome. >> >> > 4. Is there an option to fit for charges? >> No, but in https://github.com/votca/csg/pull/199 somebody tried to >> implement that in the relative entropy method, it got never merged >> though. >> >> > 5. While force matching for a long molecule, how are Van der Waals forces >> > treated within a molecule? Is the Van der Waals force excluded between all >> > beads within a molecule or just the 1-4 neighbors? I saw there was an >> > option for Boltzmann inversion but I couldn't find anything for force >> > matching. >> >> You can setup internal interaction, which csg_match can also fit at >> the same time, you can apply some kind of hybrid scheme, >> seehttp://dx.doi.org/10.1002/mats.201100011 >> >> > >> > Sorry to bother you with so many questions, Thank you very much for your >> > help. >> No worries! >> >> Christoph >> > >> > On Wed, Apr 10, 2019 at 1:05 PM Christoph Junghans <[email protected]> >> > wrote: >> >> >> >> On Wed, Apr 10, 2019 at 11:01 AM Aditi Khot <[email protected]> wrote: >> >> > >> >> > Hi, >> >> > >> >> > I am trying to perform force matching for butanol one bead mapping. >> >> > This is the command I run >> >> > >> >> > csg_fmatch --top topology.xml --trj AAtrajectory.h5 --options >> >> > fmatch.xml --cg mapping.xml >> >> > >> >> > >> >> > And this is the error I get: >> >> > >> >> > terminate called after throwing an instance of 'std::runtime_error' >> >> > >> >> > what(): constrained_qrsolve_zero_column_in_matrix >> >> > >> >> > Aborted >> >> This just means the QR solve of the force matrix failed. There might >> >> be not enough statistics in each bin. >> >> So you could either make the trajectory longer, the bins bigger or if >> >> the minimum of the interactions larger (in case you have not enough >> >> statistics there.) >> >> >> >> Christoph >> >> >> >> >> >> > >> >> > >> >> > I also tried, mapping the forces using the command below. The forces in >> >> > the output.dump file seem to be correct. >> >> > >> >> > csg_map --top topology.xml --trj AAtrajectory.h5 --out output.dump >> >> > --cg mapping.xml --force >> >> > >> >> > >> >> > I have attached the files: >> >> > https://drive.google.com/file/d/1IrEs4DfvykiZS05uy7aXKsP90e_WxHdB/view?usp=sharing. >> >> > Please let me know what might be wrong. Thank you so much! >> >> > >> >> > Thanks, >> >> > Aditi. >> >> > >> >> > -- >> >> > 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. >> > >> > >> > >> > -- >> > Aditi Khot, >> > Dual Degree Final Year, >> > Chemical Engineering, >> > Indian Institute of Technology, Madras. >> > >> > -- >> > 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. > > > > -- > Aditi Khot, > Dual Degree Final Year, > Chemical Engineering, > Indian Institute of Technology, Madras. > > -- > 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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