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.
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. 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