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Reverse transformation for elnedyn model
- clavila
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11 years 3 months ago #1381
by clavila
Reverse transformation for elnedyn model was created by clavila
Dear all,
I was wondering if the protocol presented in the reverse_transformation tutorial also applies to CG models generated using ELNEDYN. My concern is that the mapping of the AA to CG beads might not be the same. I think the backbone bead in MARTINI maps to the center of mass of N, CA, C, O, while in ELNEDYN it maps to the coordinates of CA alone.
I am getting LINCS warning at each step of the SA in a CG->AA transformation of an ELNEDYN protein complex and I was wondering if this was the reason.
Cheers,
Cesar
I was wondering if the protocol presented in the reverse_transformation tutorial also applies to CG models generated using ELNEDYN. My concern is that the mapping of the AA to CG beads might not be the same. I think the backbone bead in MARTINI maps to the center of mass of N, CA, C, O, while in ELNEDYN it maps to the coordinates of CA alone.
I am getting LINCS warning at each step of the SA in a CG->AA transformation of an ELNEDYN protein complex and I was wondering if this was the reason.
Cheers,
Cesar
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- xavier
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11 years 1 month ago #1438
by xavier
Replied by xavier on topic Reverse transformation for elnedyn model
Hi, sorry for the delay in answering.
We have performed a few reserve transformations with the MARTINI force field coupled with ElNeDyn. The difference of the mapping of the Backbone you mention appeared not to be a problem.
The lincs warning were inevitable, they are inerrent to the atomistic force field. The NH group have very fast vibrations. Did you try to reduce the time step to 1 fs?
Did you fix your problem?
We have performed a few reserve transformations with the MARTINI force field coupled with ElNeDyn. The difference of the mapping of the Backbone you mention appeared not to be a problem.
The lincs warning were inevitable, they are inerrent to the atomistic force field. The NH group have very fast vibrations. Did you try to reduce the time step to 1 fs?
Did you fix your problem?
clavila wrote: Dear all,
I was wondering if the protocol presented in the reverse_transformation tutorial also applies to CG models generated using ELNEDYN. My concern is that the mapping of the AA to CG beads might not be the same. I think the backbone bead in MARTINI maps to the center of mass of N, CA, C, O, while in ELNEDYN it maps to the coordinates of CA alone.
I am getting LINCS warning at each step of the SA in a CG->AA transformation of an ELNEDYN protein complex and I was wondering if this was the reason.
Cheers,
Cesar
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- clavila
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11 years 1 month ago #1462
by clavila
Replied by clavila on topic Reverse transformation for elnedyn model
Hi Xavier,
thanks for your reply. You were right, using 1 fs timestep solved the problem. I still got some LINCS warnings from time to time, but the simulation was able to reach to the end.
thanks for your reply. You were right, using 1 fs timestep solved the problem. I still got some LINCS warnings from time to time, but the simulation was able to reach to the end.
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11 years 1 month ago #1463
by xavier
Replied by xavier on topic Reverse transformation for elnedyn model
Cool, tks for reporting.
XAvier.
XAvier.
clavila wrote: Hi Xavier,
thanks for your reply. You were right, using 1 fs timestep solved the problem. I still got some LINCS warnings from time to time, but the simulation was able to reach to the end.
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