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 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.

Reply via email to