2016-08-31 12:24 GMT-06:00 Chang Woon Jang <[email protected]>: > 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 <[email protected]> > wrote: >> >> 2016-08-31 10:58 GMT-06:00 Chang Woon Jang <[email protected]>: >> > 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 >> > <[email protected]> >> > wrote: >> >> >> >> 2016-08-31 9:25 GMT-06:00 Chang Woon Jang <[email protected]>: >> >> > 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 >> >> > <[email protected]> >> >> > wrote: >> >> >> >> >> >> 2016-08-31 8:43 GMT-06:00 Chang Woon Jang <[email protected]>: >> >> >> > 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 >> >> >> > <[email protected]> >> >> >> > 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: [email protected] >> >> >> > >> >> >> > -- >> >> >> > 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. >> >> > >> >> > >> >> > >> >> > -- >> >> > 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. >> > >> > >> > >> > >> > -- >> > 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: [email protected] >> > >> > -- >> > 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. > > > > > -- > 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: [email protected] > > -- > 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. 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