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Issues with neighboring glycines
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13 years 1 month ago #616
by joshua_roc
Issues with neighboring glycines was created by joshua_roc
I have heard rumor that there may be issues with MARTINI when glycines are side-by-side in a sequence. I'd had issues with my systems crashing frequently at timesteps greater than 10fs, and it has been suggested to me that neighboring glycines, because the beads are very attractive, may be compressed and the resulting force causes crashes.
Any truth to this?
Any truth to this?
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13 years 1 month ago #618
by xavier
Replied by xavier on topic Issues with neighboring glycines
The rumor is right :))
There is indeed an issue with glycine and alanines repeats in a coil region.
The force constant of the backbone bond is set to a small value (400 I believe) to allow flexibility. The non-bonded interactions are relatively strong in a coil as the bead type is P5. It results that the non-bonded interactions between residues i and i+2 (the second neighbor) dominate the bonded terms between consecutive G/A backbone beads.
This can be solved by increasing the force constant of the bond between coil backbone beads. This will soon be incorporated in the official version of the script. In the mean time you can do it within your topology.
This should solve the instability of your system.
There is indeed an issue with glycine and alanines repeats in a coil region.
The force constant of the backbone bond is set to a small value (400 I believe) to allow flexibility. The non-bonded interactions are relatively strong in a coil as the bead type is P5. It results that the non-bonded interactions between residues i and i+2 (the second neighbor) dominate the bonded terms between consecutive G/A backbone beads.
This can be solved by increasing the force constant of the bond between coil backbone beads. This will soon be incorporated in the official version of the script. In the mean time you can do it within your topology.
This should solve the instability of your system.
joshua_roc wrote: I have heard rumor that there may be issues with MARTINI when glycines are side-by-side in a sequence. I'd had issues with my systems crashing frequently at timesteps greater than 10fs, and it has been suggested to me that neighboring glycines, because the beads are very attractive, may be compressed and the resulting force causes crashes.
Any truth to this?
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13 years 1 month ago #619
by joshua_roc
Replied by joshua_roc on topic Issues with neighboring glycines
Thanks for the fast response!
Do you have a suggested value for the force constant?
Do you have a suggested value for the force constant?
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13 years 1 month ago #620
by xavier
Not precisely. That is one thing that has to be looked at. But my guess is that something around 1000 should be fine. But again this has to be tried ... you may want to try and report back. That would be useful :))
Tks.
Replied by xavier on topic Issues with neighboring glycines
joshua_roc wrote: Thanks for the fast response!
Do you have a suggested value for the force constant?
Not precisely. That is one thing that has to be looked at. But my guess is that something around 1000 should be fine. But again this has to be tried ... you may want to try and report back. That would be useful :))
Tks.
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