Hi Sikandar, I'm a little confused, I am already telling Gromacs to use *table.xvg by setting vdwtype = user and energygrp_table = PEO PEO PBO PBO PEO PBO. I thought that this was the tabulated potential of mean force (in the first run). Do you mean I should produce my own tables like this: http://www.gromacs.org/Documentation/How-tos/Tabulated_Potentials using values for sigma and epsilon read from my current explosion inducing PMF tables?
I didn't think that the cut-off would cause the system to blow up either, the reason why I'm using such a short one is because my RDFs don't quite converge to 1 so it seemed like a better idea to try and fit just the first peak, at least initially. Thanks a lot, Dan. On Wednesday, 28 January 2015 21:50:55 UTC, sikandar wrote: > > 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] > <javascript:>> 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] <javascript:>. >> To post to this group, send email to [email protected] <javascript:> >> . >> 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.
