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amino acid bonds
- roshanak
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7 years 2 months ago - 7 years 2 months ago #7116
by roshanak
Replied by roshanak on topic amino acid bonds
> Are all atoms present in "1.pdb"? Especially if you got it from X-ray
there may be some unresolved atoms.
I check my pdb file with SPDBV, it hasn't missing atom. Is it another way to doing it?
> Can you find for me the shortest distance between any two beads after
the minimization?
I don't know how to do it. Would you please explain me ?
>I try it and equilibration was done. But i see in my structure, at the top of peptides, some NC3 beads (for 7 lipids).
What does this mean?
I think what I see, is effect of pbc. is it true? I see some lipid beads (headgroup beads) placed away from other lipid beads and near peptide beads. is my explanation intelligible now?
there may be some unresolved atoms.
I check my pdb file with SPDBV, it hasn't missing atom. Is it another way to doing it?
> Can you find for me the shortest distance between any two beads after
the minimization?
I don't know how to do it. Would you please explain me ?
>I try it and equilibration was done. But i see in my structure, at the top of peptides, some NC3 beads (for 7 lipids).
What does this mean?
I think what I see, is effect of pbc. is it true? I see some lipid beads (headgroup beads) placed away from other lipid beads and near peptide beads. is my explanation intelligible now?
Last edit: 7 years 2 months ago by roshanak.
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- roshanak
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7 years 2 months ago - 7 years 2 months ago #7118
by roshanak
Replied by roshanak on topic amino acid bonds
I forgot to ask it, Is my TC groups true? (with regard to my explanation about this system)
Last edit: 7 years 2 months ago by roshanak.
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- peterkroon
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7 years 1 month ago #7133
by peterkroon
Replied by peterkroon on topic amino acid bonds
Count the atoms, and check with what it should be according to the number and type of residues
use gmx distance or gmx mindist
That would be strange. Are there bonds missing in your lipid topologies? Warp around from PBC would also be possible (do `pbc box` in vmd to visualize the boundaries)
I answered about TC groups before.
use gmx distance or gmx mindist
That would be strange. Are there bonds missing in your lipid topologies? Warp around from PBC would also be possible (do `pbc box` in vmd to visualize the boundaries)
I answered about TC groups before.
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- johnd
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7 years 1 month ago #7142
by johnd
Replied by johnd on topic amino acid bonds
A bit late to the party, but I'll throw in my two cents
1- dt=0.001 means nothing for a steep integrator; it is controlled by emstep
manual.gromacs.org/online/mdp_opt.html#em
2- I have gotten this G96 angle error before on occasion. It has only ever happened to me when I run on a cluster without using the -rdd flag when running mdrun
i.e. (to implement) mdrun -deffnm equ -nt 2 -v -rdd 1.5
Sometimes it happens 5 ns in, sometimes at 4.5 μs, and sometimes it just never happens at all
For reference, I use v5.0.4
1- dt=0.001 means nothing for a steep integrator; it is controlled by emstep
manual.gromacs.org/online/mdp_opt.html#em
2- I have gotten this G96 angle error before on occasion. It has only ever happened to me when I run on a cluster without using the -rdd flag when running mdrun
i.e. (to implement) mdrun -deffnm equ -nt 2 -v -rdd 1.5
Sometimes it happens 5 ns in, sometimes at 4.5 μs, and sometimes it just never happens at all
For reference, I use v5.0.4
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