On Thu, Apr 25, 2019 at 9:37 AM Aditi Khot <[email protected]> wrote: > > Thank you Christoph. I understand how atomistic forces without bonded > interactions are obtained, but I have a doubt in coarse-grained forces. > > So, for example, let's say there are 5 beads in the CG representation, and I > want to fit only nonbonded interaction/ hybrid FM. While fitting, there will > not be any bonded interaction. But is it assumed that the nonbonded > interactions are only among CG beads from different molecules? Or even the CG > beads within the same molecule? No, csg_fmatch cannot distinguish these contributions. The atomic trajectory only has the sum of all forces on an atom and once mapped to the CG representation it is the weighed sum. If you want to exclude some internal contributions, you will need to provide an CG trajecotory with --trj-force.
Christoph > > Thanks, > Aditi. > > On Tue, Apr 16, 2019 at 10:32 AM Christoph Junghans <[email protected]> > wrote: >> >> 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. > > > > -- > 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.
