It gave nothing in the exclusion list. I am sorry I might not have asked my doubt clearly. I mean for the CG representation the are the non bonded interactions only between intermolecular beads? Or are they between some intramolecular beads (for example. if they are 5 neighbors apart)?
Thanks, Aditi. On Thu, Apr 11, 2019 at 7:10 PM Aditi Khot <[email protected]> wrote: > Thank you! > > On Thu, Apr 11, 2019 at 4:17 PM Christoph Junghans <[email protected]> > wrote: > >> 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. >> 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. > -- 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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