2016-08-31 16:15 GMT-06:00 Chang Woon Jang <changwoonj...@gmail.com>: > Dear Christoph, > > I re-extrapolated ABA angle (table_a1.xvg). The initial distribution > of ABA angle from BI is in Figure 1. After doing "csg_call --options > options.xml --ia-type angle --ia-name angle --sloppy-tables > convert_potential gromacs input output", in the lower angle, the slope is > going down in Figure 2. > > Why is this happening? Sometimes VOTCA's automatism fail. We use the last 3 valid point to add an average for the extrapolation: <https://github.com/votca/csg/blob/master/share/scripts/inverse/potential_extrapolate.sh#L39> And in your case, that doesn't make it steep enough! You will need to do some fine-tweaking by hand-editing the file.
To repeat my questions for the third time: Are you trying to do IBI on the bonded interaction, too? Or are they fixed? Christoph > > Thank you. > > Best regards, > Changwoon Jang > > > > On Wed, Aug 31, 2016 at 5:21 PM, Christoph Junghans <jungh...@votca.org> > wrote: >> >> 2016-08-31 14:51 GMT-06:00 Chang Woon Jang <changwoonj...@gmail.com>: >> > Dear Christoph, >> > >> > It is zero at 180 degree. As you see in the figure (ABAanglehis.png - >> > supposed to be table_a1.xvg), value is zero at 180 degree. >> > >> > What I did, I removed the distribution below 1.5, then it is >> > extrapolated. >> > Is this maybe the cause of failure of the run? >> > >> > Do I need to redo csg_call based on this whole distribution instead of >> > only >> > 1.5~3.14? >> If it is zero at 180, you should make sure the potential goes to a >> high value there! >> >> Are you trying to do IBI on the bonded interaction, too? Or are they >> fixed? >> >> Christoph >> > >> > Thank you. >> > >> > Best regards, >> > Changwoon Jang >> > >> > >> > On Wed, Aug 31, 2016 at 4:16 PM, Christoph Junghans <jungh...@votca.org> >> > wrote: >> >> >> >> 2016-08-31 12:24 GMT-06:00 Chang Woon Jang <changwoonj...@gmail.com>: >> >> > Dear Christoph, >> >> > >> >> > I have tested IBI with angle potential from hexane tutorial. I >> >> > replace >> >> > hexane angle potential with table_a1.xvg in my system. In topol.top, >> >> > I >> >> > used >> >> > all tabulated angle potentials (8) instead of harmonic angles (2). >> >> Are you trying to do IBI on the bonded interaction, too? Or are they >> >> fixed? >> >> >> >> > >> >> > Now, it smoothly works. I think that the A-B-A type angle >> >> > potential >> >> > (table_a1.xvg) has a problem. >> >> > >> >> > As you said, what does that mean of "you might want to extrapolate >> >> > toward >> >> > 180 degree at bit steeper"? I would like to refine the potential of >> >> > table_a1.xvg because of the rest of potentials look fine at least IBI >> >> > running. >> >> Does the angle distribution have a non-zero value at 180 degree? >> >> >> >> Christoph >> >> > >> >> > Thank you. >> >> > >> >> > Best regards, >> >> > Changwoon Jang >> >> > >> >> > On Wed, Aug 31, 2016 at 1:30 PM, Christoph Junghans >> >> > <jungh...@votca.org> >> >> > wrote: >> >> >> >> >> >> 2016-08-31 10:58 GMT-06:00 Chang Woon Jang >> >> >> <changwoonj...@gmail.com>: >> >> >> > Dear Christoph, >> >> >> > >> >> >> > When I change only harmonic angle from tabulated angle for >> >> >> > "TDM" >> >> >> > molecule in topology file (topol.top) as follow, it smoothly now >> >> >> > works. >> >> >> > The >> >> >> > rest of bond, angle, dihedral still usethe tabulated (8) >> >> >> > potentials. >> >> >> > >> >> >> > What does this mean? Is The tabulated angle potential derived >> >> >> > for >> >> >> > TDM >> >> >> > molecule incorrect? >> >> >> I just means something isn't ok with that potential. >> >> >> Look at the angle potentials of the original VOTCA paper >> >> >> <http://dx.doi.org/10.1021/ct900369w> >> >> >> From the tables you sent yesterday, you might want to extrapolate >> >> >> toward 180 degree at bit steeper. >> >> >> >> >> >> If you are doing IBI, you don't have to use the Boltzmann inverted >> >> >> potential, you can always start from a harmonic potential as the >> >> >> initial guess. >> >> >> >> >> >> >> >> >> Christoph >> >> >> >> >> >> > >> >> >> > [ angles ] >> >> >> > 1 3 2 2 1 1.0 <--- originally 8 >> >> >> > 1 3 4 2 1 1.0 <--- originally 8 >> >> >> > 1 3 5 2 1 1.0 <--- originally 8 >> >> >> > 2 3 4 2 1 1.0 <--- originally 8 >> >> >> > 2 3 5 2 1 1.0 <--- originally 8 >> >> >> > 4 3 5 2 1 1.0 <--- originally 8 >> >> >> > >> >> >> > >> >> >> > Best regards, >> >> >> > Changwoon Jang >> >> >> > >> >> >> > >> >> >> > >> >> >> > On Wed, Aug 31, 2016 at 11:46 AM, Christoph Junghans >> >> >> > <jungh...@votca.org> >> >> >> > wrote: >> >> >> >> >> >> >> >> 2016-08-31 9:25 GMT-06:00 Chang Woon Jang >> >> >> >> <changwoonj...@gmail.com>: >> >> >> >> > Dear Christoph, >> >> >> >> > >> >> >> >> > IBI still fails few iteration later the angle is going and >> >> >> >> > coming >> >> >> >> > at >> >> >> >> > the >> >> >> >> > boundary. See the figures. I am not sure why GROMACS does not >> >> >> >> > consider >> >> >> >> > the >> >> >> >> > PBC effect. The 201-202-203 angle looks like over 180 degree. >> >> >> >> > Do >> >> >> >> > you >> >> >> >> > have >> >> >> >> > any suggestion? >> >> >> >> Well, not really. I guess it is time to debug your topology! >> >> >> >> I would start with using some harmonic interactions for all >> >> >> >> angles >> >> >> >> (with approximately the right mean and width) and replace them >> >> >> >> one >> >> >> >> by >> >> >> >> one to see, which one make the simulation crash. >> >> >> >> >> >> >> >> Christoph >> >> >> >> > >> >> >> >> > Thank you. >> >> >> >> > >> >> >> >> > Best regards, >> >> >> >> > Changwoon Jang >> >> >> >> > >> >> >> >> > On Wed, Aug 31, 2016 at 11:05 AM, Christoph Junghans >> >> >> >> > <jungh...@votca.org> >> >> >> >> > wrote: >> >> >> >> >> >> >> >> >> >> 2016-08-31 8:43 GMT-06:00 Chang Woon Jang >> >> >> >> >> <changwoonj...@gmail.com>: >> >> >> >> >> > Dear Votca Users, >> >> >> >> >> > >> >> >> >> >> > I have missed the figures. Figure 1 is initial >> >> >> >> >> > configuration. >> >> >> >> >> > Figure >> >> >> >> >> > 2 is >> >> >> >> >> > the final iteration (1000 iteration) right before the ibi >> >> >> >> >> > fails. >> >> >> >> >> > >> >> >> >> >> > Thank you. >> >> >> >> >> > >> >> >> >> >> > Best regards, >> >> >> >> >> > Changwoon Jang >> >> >> >> >> > >> >> >> >> >> > >> >> >> >> >> > On Wed, Aug 31, 2016 at 10:35 AM, Chang Woon Jang >> >> >> >> >> > <changwoonj...@gmail.com> >> >> >> >> >> > wrote: >> >> >> >> >> >> >> >> >> >> >> >> Dear Votca Users, >> >> >> >> >> >> >> >> >> >> >> >> I have a question about creating initial configuration >> >> >> >> >> >> of >> >> >> >> >> >> the >> >> >> >> >> >> system. >> >> >> >> >> >> >> >> >> >> >> >> 1. Full atomistic simulation ---- I have run full >> >> >> >> >> >> atomistic >> >> >> >> >> >> simulations of polymer system with OPLS-AA force field. >> >> >> >> >> >> Then, >> >> >> >> >> >> it >> >> >> >> >> >> (low >> >> >> >> >> >> density system) was equilibrated with NVT and NPT >> >> >> >> >> >> simulation >> >> >> >> >> >> for >> >> >> >> >> >> 50 >> >> >> >> >> >> ns. >> >> >> >> >> >> Thus, the box under PBC is shrinked from 10nm to about 5nm. >> >> >> >> >> >> >> >> >> >> >> >> 2. Then, I used the final configuration (confout.gro) >> >> >> >> >> >> in >> >> >> >> >> >> order >> >> >> >> >> >> to >> >> >> >> >> >> map >> >> >> >> >> >> the atomistic system into Coarse-grained system. >> >> >> >> >> >> >> >> >> >> >> >> I used this CG system for IBI in order to get >> >> >> >> >> >> non-bonded >> >> >> >> >> >> potentials. >> >> >> >> >> >> However, when I run IBI, I think that some of angle are >> >> >> >> >> >> blowing >> >> >> >> >> >> up >> >> >> >> >> >> and >> >> >> >> >> >> the >> >> >> >> >> >> ibi run finally fail in the beginning. I checked CG >> >> >> >> >> >> trajectory. >> >> >> >> >> >> An >> >> >> >> >> >> angle >> >> >> >> >> >> seem to be blowing up as shown in figure. >> >> >> >> >> >> >> >> >> >> >> >> I think this is ok if the system is under PBC. But the >> >> >> >> >> >> error >> >> >> >> >> >> message >> >> >> >> >> >> keeps indicate this angle has a problem. >> >> >> >> >> You might want to run >> >> >> >> >> $ gmx trjconv -f conf_in.gro -o conf_out.gro -pbc mol >> >> >> >> >> to make molecule whole. >> >> >> >> >> >> >> >> >> >> Christoph >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> Therefore, I am asking for how you create the initial CG >> >> >> >> >> >> system >> >> >> >> >> >> all >> >> >> >> >> >> beads are inside box but not at the boundary. >> >> >> >> >> >> >> >> >> >> >> >> Thank you. >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> **************************************************************************************************** >> >> >> >> >> >> Not all bonded interactions have been properly assigned to >> >> >> >> >> >> the >> >> >> >> >> >> domain >> >> >> >> >> >> decomposition cells >> >> >> >> >> >> >> >> >> >> >> >> A list of missing interactions: >> >> >> >> >> >> Tab. Angles of 856 missing 1 >> >> >> >> >> >> >> >> >> >> >> >> Molecule type 'TDM' >> >> >> >> >> >> the first 10 missing interactions, except for exclusions: >> >> >> >> >> >> Tab. Angles atoms 1 3 2 global 201 >> >> >> >> >> >> 203 >> >> >> >> >> >> 202 >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> ****************************************************************************************************** >> >> >> >> >> >> >> >> >> >> >> >> Best regards, >> >> >> >> >> >> Changwoon Jang, >> >> >> >> >> >> >> >> >> >> >> > >> >> >> >> >> > >> >> >> >> >> > >> >> >> >> >> > -- >> >> >> >> >> > Best regards, >> >> >> >> >> > Changwoon Jang, >> >> >> >> >> > >> >> >> >> >> > Postdoctoral Research Fellow >> >> >> >> >> > Department of Chemical & Biological Engineering, Drexel >> >> >> >> >> > University >> >> >> >> >> > 3141 Chestnut Street, Philadelphia, PA 19104 >> >> >> >> >> > >> >> >> >> >> > Voice: (662) 617-2267 >> >> >> >> >> > E-mail: cj...@drexel.edu >> >> >> >> >> > >> >> >> >> >> > -- >> >> >> >> >> > You received this message because you are subscribed to the >> 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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 votca+unsubscr...@googlegroups.com. >> >> >> >> To post to this group, send email to votca@googlegroups.com. >> >> >> >> Visit this group at https://groups.google.com/group/votca. >> >> >> >> For more options, visit https://groups.google.com/d/optout. >> >> >> > >> >> >> > >> >> >> > >> >> >> > >> >> >> > -- >> >> >> > Best regards, >> >> >> > Changwoon Jang, >> >> >> > >> >> >> > Postdoctoral Research Fellow >> >> >> > Department of Chemical & Biological Engineering, Drexel University >> >> >> > 3141 Chestnut Street, Philadelphia, PA 19104 >> >> >> > >> >> >> > Voice: (662) 617-2267 >> >> >> > E-mail: cj...@drexel.edu >> >> >> > >> >> >> > -- >> >> >> > You received this 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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 votca+unsubscr...@googlegroups.com. >> >> To post to this group, send email to votca@googlegroups.com. >> >> Visit this group at https://groups.google.com/group/votca. >> >> For more options, visit https://groups.google.com/d/optout. >> > >> > >> > >> > >> > -- >> > Best regards, >> > Changwoon Jang, >> > >> > Postdoctoral Research Fellow >> > Department of Chemical & Biological Engineering, Drexel University >> > 3141 Chestnut Street, Philadelphia, PA 19104 >> > >> > Voice: (662) 617-2267 >> > E-mail: cj...@drexel.edu >> > >> > -- >> > 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 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