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? If so, would you please let me know how I can include it without redoing the simulation? 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 [email protected]. To post to this group, send email to [email protected]. Visit this group at https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
