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. -- You received this message because you are subscribed to the Google Groups "votca" group. 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