On Sun, Apr 14, 2019 at 10:14 AM Aditi Khot <[email protected]> wrote: > > 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)? It the list is empty, nothing is excluded and hence it should force-match intramoleclar beads as well. If you don't want that just setup an interaction between the beads in the mapping file.
Christoph > > 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. > 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.
