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? 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 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