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.
