Hi Christoph,
Thank you for your response.

As I pointed out, my goal is to do BI for bonded and IBI for nonbonded; for 
the BI bonded, I was wondering If I should consider periodicity for the 
dihedrals or angle in csg_boltzmann, I mean "tab set periodic 0" or "tab 
set periodic 1" as they give  different dihedral.pot.ib?

How about if both of the bonded and nonbonded are treated via IBI?

Thank you.

Regards,
Alex

On Friday, April 13, 2018 at 12:31:32 PM UTC-4, Christoph Junghans wrote:
>
> On Fri, Apr 13, 2018 at 8:57 AM, Alexander Alexander 
> <alexand...@gmail.com <javascript:>> 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 
> > 
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>
> -- 
> Christoph Junghans 
> Web: http://www.compphys.de 
>

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