Hi all, it seems that the distribution is not converging. My .top and grompp.mdp files are set just has Valentina indicated me but the simulations are still not giving the results that are expected.
I'm still working on it but any idea or tip will be infinitely appreciated. All the best, Sacha On Oct 21, 5:08 pm, Sacha Mould <[email protected]> wrote: > I appreciate so much your advice Valentina. I will follow your > indications and let's see what i get. > > All the best!!!! :) > > Sacha > > On Oct 21, 3:38 pm, Valentina <[email protected]> wrote: > > > > > > > > > Hi Sacha, I had similar problem at first, just to realise after that > > in my grompp.mdp, settings.xml and index.ndx I have not specified > > correctly non-bonded groups & correct names. Here is what I did to get > > mines working, so mb good to double check yours are all fine too. > > > So tabulated bond and angle are specified in the topol.top file like > > this: > > > [ bonds ] > > 1 2 8 1 1 ; corresponds to table_b1.xvg > > 1 6 8 1 2 ; corresponds to table_b2.xvg > > 1 5 8 1 2 ; corresponds to table_b2.xvg > > 2 3 8 1 2 ; corresponds to table_b2.xvg > > 2 4 8 1 2 ; corresponds to table_b2.xvg > > > [ angles ] > > 4 2 3 8 1 1 ; corresponds to table_a1.xvg > > 5 1 6 8 1 1 ; corresponds to table_a1.xvg > > 6 1 2 8 1 2 ; corresponds to table_a2.xvg > > 5 1 2 8 1 2 ; corresponds to table_a2.xvg > > 3 2 1 8 1 2 ; corresponds to table_a2.xvg > > 4 2 1 8 1 2 ; corresponds to table_a2.xvg > > > And non-bonded ones in grompp.mdp like this, here is my example, yours > > seem to be simpler: > > I have 2 types of energy groups B and M and I have 3 tables of the > > interactions: B-B B-M and M-M that are tabulated as table_B_B.xvg > > table_B_M.xvg table_M_M.xvg respectively. > > > energygrps = B M ; groups to write to energy > > file > > energygrp_table = B B B M M M ; corresponds > > > That should match what you have in settings.xml: > > > <non-bonded> > > ... > > <inverse> > > ... > > <gromacs> > > <table>table_M_M.xvg</table> similar for B-M and B-B > > </gromacs> > > </inverse> > > </non-bonded> > > > Additionally you will need a correct index.ndx file that you can make > > by > > $ make_ndx -f conf.gro > > and when it asks you what groups (in my case) i do: > > a B* > > a M* > > q > > > then I have to go into the index.ndx and manually remove * from [ B* ] > > and [ M* ] to make them [ B ] and [ M ]. Mb there is other way around > > this part, but thats what works for me. > > > May be this will help:) > > V > > > On Oct 21, 1:00 pm, Sacha Mould <[email protected]> wrote: > > > > Hi all, > > > > i'm having problems with my iBI simulation results, the distribution > > > function is not converging after 150 iterations: > > > > i'm trying to run coase-graining simulations of polyethylene using IBI > > > method. The atomistic system consisted on 10 chain molecules with 50 > > > DP simulated with LAMMPS using the COMPASS forcefield from where i > > > dumped the RDF, bond, and angle distributions. Either RDF and bond > > > distribution obtained from atomistic simulation where similar in shape > > > with the ones obtained for hexane in "Macromol. Theory Simul. 20, pp > > > 472-477 (2011)". For the IBI simulation i want to map 5 monomers into > > > a coarse-grained particle resulting on a system with 10 chains with 10 > > > beads per chain. I generated all the files required for the IBI > > > simulation, including exclusions file, using Votca tools. Angle and > > > bond interactions (table_a1.xvg and table_b1.xvg) where obtained by > > > Boltzmann inverting the distribution functions and then using > > > "csg_call convert_potential xvg" script. For non-bonded potential i > > > let Votca to do the inversion after calling "csg_inverse". I'm > > > assuming that all the particles are of the same type, which means that > > > terminal and inner chain particles are equal and the terminal > > > hydrogens on the methylenes are neglected. In the grompp file i set a > > > time-step of 1 ps and a simulation time of 1ns using stochastic > > > dynamics integrator at 450K. The cutoff where set to 1.5 nm. At this > > > moment i'm not using any kind of pressure correction and after each > > > iteration the distribution function is smoothed twice. > > > > With this setup, after running IBI the results don't converge, the > > > distribution function that i'm obtaining at the end of each iteration > > > show strange shapes and the convergence values are always in the range > > > of 0.36 - 7. > > > Other thing that concerns me is on how i should extrapolate to the > > > right the bonded potential. The atosmistic results gives me a bonded > > > distribution that goes to r=0.29 nm, the bond length of the coarse- > > > grained system is much higher than this, so i need to extrapolate the > > > bonded potential to higher values of r. I'm using quadratic function > > > to extrapolate the table, but i'm not quite sure in which extent these > > > extrapolated values are feasible. > > > > I wonder if someone can help me. Is anything wrong with my setup??? Is > > > there something missing that i should account with?? > > > > Thanks a lot in advance, > > > > Sacha -- You received this message because you are subscribed to the Google Groups "votca" group. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/votca?hl=en.
