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.
