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? Thank you. Best regards, Changwoon Jang On Wed, Aug 31, 2016 at 4:16 PM, Christoph Junghans <[email protected]> wrote: > 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. > 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. 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