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.
