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.
