On Fri, Apr 13, 2018 at 8:57 AM, Alexander Alexander <alexanderwie...@gmail.com> wrote: > > Dear all, > > In CG parametrisation of one of my molecule which has 45 atoms, using BI for > bonded and IBI for nonbonded parameters, a 900 ns simulation of the single > molecule in vacuum has been already completed while I forgot including the > exclusions list gotten from csg_boltzmann in to my topol.top file. In > mapping I have 5 bead in three type. > > Here is the exclusions list give by csg_boltzmann: > > csg_boltzmann --top prd.tpr --cg map.xml --excl exclusions.txt > > # atomistic: VRLD cg: VRLD cgmap: mapping.xml > 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 > 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 > 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 > 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 > 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 > 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 > 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 > 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 > 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 > 32 33 34 35 36 37 38 39 40 41 42 43 44 45 > 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 > 33 34 35 36 37 38 39 40 41 42 43 44 45 > 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 > 33 34 35 36 37 38 39 40 41 42 43 44 45 > 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 > 34 35 36 37 38 39 40 41 42 43 44 45 > 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 > 35 36 37 38 39 40 41 42 43 44 45 > > And here is what csg_dump gives me: > csg_dump --cg map.xml --top prd.tpr --excl > > I have 45 beads in 1 molecules > I have 5 beads in 1 molecules for the coarsegraining > List of exclusions: > 1 2 3 4 > 2 3 4 5 > 3 4 5 > 4 5 > > First of all, I was wondering if it is important for such system to include > the exclusion list in topol.top for this molecule? First of all, you only need the exclusions for the single molecule in vacuum run at the atomistic scale. You usually don't need exclusions on the coarse-graining level as gromacs excluded all atoms, which interaction via a bonded interaction from non-bonded automatically. (see the gromacs manual for details)
You can check you exclusions with gmx dump or: $ csg_dump --top topol.tpr --excl > If so, would you please let me know how I can include it without redoing the > simulation? If you forgot to include the block in the atomistic run, you will need to rerun the whole simulation, but for a single molecule that should take too long. Christoph > probably one way is to generate a new case.tpr file including the exclusion > list and then continuing the simulation for a short time with "-cpi prd.cpt > -append" so that we do not loose the 900 ns of simulation, can you please > confirm/correct me? > > Thank you. > Regards, > Alex > > -- > 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 votca+unsubscr...@googlegroups.com. > To post to this group, send email to votca@googlegroups.com. > Visit this group at https://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 votca+unsubscr...@googlegroups.com. To post to this group, send email to votca@googlegroups.com. Visit this group at https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
