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Beads are scattering
- robraunjp
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14 years 3 weeks ago #342
by robraunjp
Beads are scattering was created by robraunjp
Hello all
I am facing quite a problem with my CG protein simulation.
I successfuly simulated a monomeric form of my protein, and a trimeric form of it as well. Now I am simulating a bacterial equivalent of the monomeric form, but this bacterial protein is itself, a trimer (and a trimer of this equivalent would be a 'trimer of trimers'). My problem is that this bacterial protein seems to "explode" soon after the MD run starts. It is not an explosion of the 'Lincs warning' sort. It seems that the protein has no bonding whatsoever. Comparing the monomeric protein(functional) and the bacterial trimer ("explosive") itps, the explosive itp has no short or long elastic bonds.
Suggestions?
Thank you in advance
I am facing quite a problem with my CG protein simulation.
I successfuly simulated a monomeric form of my protein, and a trimeric form of it as well. Now I am simulating a bacterial equivalent of the monomeric form, but this bacterial protein is itself, a trimer (and a trimer of this equivalent would be a 'trimer of trimers'). My problem is that this bacterial protein seems to "explode" soon after the MD run starts. It is not an explosion of the 'Lincs warning' sort. It seems that the protein has no bonding whatsoever. Comparing the monomeric protein(functional) and the bacterial trimer ("explosive") itps, the explosive itp has no short or long elastic bonds.
Suggestions?
Thank you in advance
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- durbignon
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14 years 3 weeks ago #343
by durbignon
Replied by durbignon on topic Beads are scattering
You are kidding, right?! Did you check all the parameters?!
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- robraunjp
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14 years 3 weeks ago #346
by robraunjp
Replied by robraunjp on topic Beads are scattering
No, I wasn't kidding.
And yes, I intend to delete the original post as soon as I can.
After checking all my input files I found I tiny error on my sequence file that led to a topology file with no bond data in it. That was the origin of my CG MD mistake.
Thanks (and sorry for the inconvenience).
And yes, I intend to delete the original post as soon as I can.
After checking all my input files I found I tiny error on my sequence file that led to a topology file with no bond data in it. That was the origin of my CG MD mistake.
Thanks (and sorry for the inconvenience).
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- xavier
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14 years 3 weeks ago #347
by xavier
Replied by xavier on topic Beads are scattering
Well no inconvenience here. It is place to put your problems and try to get answers to fix them.
I am not sure which Martini you are using ... with the regular version for proteins you might expect a deviation from your starting structure. It will depend a lot on the structural topology of your system.
If your problem is not solved, please give more details on your system, topology and the way you obtained it.
XAvier.
I am not sure which Martini you are using ... with the regular version for proteins you might expect a deviation from your starting structure. It will depend a lot on the structural topology of your system.
If your problem is not solved, please give more details on your system, topology and the way you obtained it.
XAvier.
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