Hi Dan, As Christoph suggested, the initial guesses from RDF inversion may be an issue, so try using simple LJ potential (the default LJ from table.xvg). Also, I am not sure why are you cutting choosing the cut-off 0.75 nm based on the first minima in the RDF. Can you try using the the same cut-off as for the LJ interaction in your reference AA system? Anyway, I dont think cut-off could be causing the simulation to blow-up, initial potential guesses could be the main cause.
Best, Sikandar On Wed, Jan 28, 2015 at 12:18 PM, Daniel Allen <[email protected]> wrote: > It is the nb potential which is problematic. This seems so strange, the > functions seem fine and exactly what you would expect from smooth well > sampled RDFs. What is even more puzzling is that the nb energy breaks in > just one time step. I have printed out energy information every timestep: > > Step Time Lambda > 4 0.00400 0.00000 > > Energies (kJ/mol) > Tab. Bonds Tab. Angles Tab. Dih. LJ (SR) Coulomb (SR) > 1.20852e+04 3.70247e+04 9.51537e+03 -7.67663e+05 0.00000e+00 > Potential Kinetic En. Total Energy Temperature Pressure (bar) > -7.09038e+05 2.99711e+04 -6.79067e+05 3.16241e+02 -3.31874e+04 > > Step Time Lambda > 5 0.00500 0.00000 > > Energies (kJ/mol) > Tab. Bonds Tab. Angles Tab. Dih. LJ (SR) Coulomb (SR) > 1.20860e+04 3.70238e+04 9.51379e+03 -nan 0.00000e+00 > > So after integration step 4 the LJ energy is -7.67663e+05 but after the > next it is -nan. In past trials with this system today the LJ energy jumps > to ~10^213 in just one step. > > If the configuration was bad then surely the energy would be very large > (and positive) from the first step? > > Any ideas what might cause it to jump like this so suddenly? I would > understand if the LJ energy increased monotonically but it seems stable > (admittedly for an embarrassingly short amount of time) and then breaks. > > > Thanks again, > > Dan. > > > > On Wednesday, 28 January 2015 17:30:20 UTC, Christoph Junghans wrote: >> >> 2015-01-28 9:11 GMT-07:00 Daniel Allen <[email protected]>: >> > Hi Christoph, >> > >> > thanks for your prompt reply. Sorry I should have been more clear, the >> > system is blowing up on the very first CG run using the initial guesses >> for >> > potentials. I realise that you could say the initial configuration must >> be >> > bad however I don't think it'll be any worse than any other snapshot >> from >> > the reference simulation given that the bilayer is stable during this. >> That usually means one of the initial guesses or the >> Boltzmann-inverted potential (when no initial potentials are given) is >> bad. >> You can look at the energy file to see, which contribution to the >> energy blows up. >> Or replace the potential one by one by a Lennard Jones to find the bad >> one. >> >> Christoph >> >> > >> > Thanks for your help, >> > >> > Dan. >> > >> > On Wednesday, 28 January 2015 15:49:53 UTC, Christoph Junghans wrote: >> >> >> >> 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. >> >> >> >> -- >> 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. > -- 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.
