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.
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.
