2015-01-28 7:45 GMT-07:00 Daniel Allen <[email protected]>: > Hello, > > I am trying to perform IBI on a bilayer formed of some polymers. I have > obtained distributions for non-bonded and bonded interactions from csg_stat > and feed these into csg_inverse in *dist.tgt files. I am not currently > iterating bonded interactions, just using csg_inverse to produce tabulated > potentials (bonds, angles, dihedrals). > > My RDFs do not quite converge to 1 as my reference system is not homogeneous > so I am cutting off interactions at the first minimum in the RDFs (at > approximately 0.75 nm). > > After about 10 integration steps in the first iteration, the simulation > blows up. The initial configuration is the last snapshot of my atomistic > reference simulation mapped onto CG representation. > > I have looked at the nb potentials (they seem reasonable) and have run a > script to determine the shortest distance between 2 non-bonded beads in my > initial conf.gro that I feed in as the starting state. The shortest distance > is 0.328 nm and sigma for that pairwise interaction is 0.41 nm. This would > result in an interaction energy of ~12.8 kJ/mol which doesn't seem > ridiculously high? > > Any ideas how to move past this? I could try using a different starting > state but I fear that any snapshots from the reference system will have pair > distances < sigma. It is really hard to say how to overcome this, but I have more general list of advice: 1.) Scale the update 2.) Change the update sequence if you have multiple interactions 3.) Use last configuration from the previous step ("laststep") as initial configuration 4.) Do a pre simulation in each iteration step (pre_simulation) to minimize the initial configuration 5.) Increase the min to only update parts of the potential 6.) Longer coarse-grained simulations 7.) Apply a transformation on the rdf before doing the update 8.) Use an initial guess (pot.in) on a bigger interval with premolded structure
Christoph > > > Thanks in advance, > > Dan. > > -- > 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 http://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 http://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
