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Bead weight
- nareshthota
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11 years 8 months ago #1071
by nareshthota
Bead weight was created by nareshthota
Hi All
When CG bead represents the four atoms, the water beads have equal weight of 72. In case of protein and aminoacid beads does all the beads bear the same weight of 72?? If not how to calculate each different bead mass?? Can somebody specify.
Thanks in Advance
Naresh
When CG bead represents the four atoms, the water beads have equal weight of 72. In case of protein and aminoacid beads does all the beads bear the same weight of 72?? If not how to calculate each different bead mass?? Can somebody specify.
Thanks in Advance
Naresh
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- djurre
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11 years 8 months ago #1072
by djurre
Replied by djurre on topic Bead weight
The 'correct' mass of the beads in (for example) a protein, is indeed not always 72. You could calculate the mass by just adding up the masses of all the underlying atoms. Two things you should realize:
1) Lower masses might mean a numerically less stable simulation, so you might have to use a smaller timestep.
2) The different masses will only effect the dynamics of your system. Since dynamics (for example diffusion) are hard to interpret in Course Grain simulations, changing the masses to their exact mass might not be better.
There for keeping all mass at 72 (or 45 for s-beads) is probably better.
1) Lower masses might mean a numerically less stable simulation, so you might have to use a smaller timestep.
2) The different masses will only effect the dynamics of your system. Since dynamics (for example diffusion) are hard to interpret in Course Grain simulations, changing the masses to their exact mass might not be better.
There for keeping all mass at 72 (or 45 for s-beads) is probably better.
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- nareshthota
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11 years 8 months ago #1073
by nareshthota
Replied by nareshthota on topic Bead weight
Dear djurre,
Thanks for your reply. I was thinking the same.I have one doubt on this. Does the side chains represent as S beads. For example my topology contains some lines like this
" 78 P5 27 LYS BB 78 0.0000 ; C
79 C3 27 LYS SC1 79 0.0000 ; C
80 Qd 27 LYS SC2 80 1.0000 ; C
81 P5 28 LYS BB 81 0.0000 ; C
82 C3 28 LYS SC1 82 0.0000 ; C
83 Qd 28 LYS SC2 83 1.0000 ; C
84 P5 29 LYS BB 84 0.0000 ; C
85 C3 29 LYS SC1 85 0.0000 ; C
86 Qd 29 LYS SC2 86 1.0000 ; C"
So in this what are S type beads. Can you please specify?? Or is it the Second column you need to take into consideration for S type bead classification??
Thanks in Advance
Naresh
Thanks for your reply. I was thinking the same.I have one doubt on this. Does the side chains represent as S beads. For example my topology contains some lines like this
" 78 P5 27 LYS BB 78 0.0000 ; C
79 C3 27 LYS SC1 79 0.0000 ; C
80 Qd 27 LYS SC2 80 1.0000 ; C
81 P5 28 LYS BB 81 0.0000 ; C
82 C3 28 LYS SC1 82 0.0000 ; C
83 Qd 28 LYS SC2 83 1.0000 ; C
84 P5 29 LYS BB 84 0.0000 ; C
85 C3 29 LYS SC1 85 0.0000 ; C
86 Qd 29 LYS SC2 86 1.0000 ; C"
So in this what are S type beads. Can you please specify?? Or is it the Second column you need to take into consideration for S type bead classification??
Thanks in Advance
Naresh
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- djurre
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11 years 8 months ago #1074
by djurre
Replied by djurre on topic Bead weight
The second column does indeed specify the bead type (in this case you only have normal beads, there are no s-type beads). The 5th column (BB, SC1, SC2) are the bead names, used to put names in gro/pdb files, create index files and for example to select certain atoms in VMD.
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- nareshthota
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11 years 8 months ago #1075
by nareshthota
Replied by nareshthota on topic Bead weight
Thanks djurre now i am clear on this.
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