On Mon, Apr 15, 2019 at 3:01 PM Aditi Khot <[email protected]> wrote: > > Thank you! > But I don't want to fit for the bonded interactions, like in the hybrid > method you mentioned earlier. I referred the hexane hybrid_force-matching > example in csg-tutorials, no bonded interactions are set up and only non > bonded interactions are fit to. I just wanted to be sure that the non bonded > interactions are not calculated for intramolecular beads in this case. Sorry > for bothering with the same question again. > Ok understood, if you look at: https://github.com/votca/csg-tutorials/blob/master/hexane/hybrid_force_matching/run.sh#L10 you will see the trick is that for hybrid force matching, we do a rerun with a new topology file with extra exclusions: https://github.com/votca/csg-tutorials/blob/master/hexane/hybrid_force_matching/topol.top#L33
And then of course, the matching is only performed on the part, which are left. Cheers, Christoph > > > On Sun, Apr 14, 2019 at 5:55 PM Christoph Junghans <[email protected]> wrote: >> >> 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. > > > > -- > 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.
