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Simulated annealing error
- bt12d026
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11 years 10 hours ago - 11 years 10 hours ago #1549
by bt12d026
Simulated annealing error was created by bt12d026
Dear all,
I was reverse transforming my CG system to AA. My system contains lipids. I am following the reverse transformation tutorial. When I am doing simulated annealing, I am getting the following error.
Warning: 1-4 interaction between 1832 and 1853 at distance 1.219 which is larger than the 1-4 table size 1.200 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
step 0
Program mdrun, VERSION 3.3.1
Source code file: nsgrid.c, line: 226
Range checking error:
Explanation: During neighborsearching, we assign each particle to a grid
based on its coordinates. If your system contains collisions or parameter
errors that give particles very high velocities you might end up with some
coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
put these on a grid, so this is usually where we detect those errors.
Make sure your system is properly energy-minimized and that the potential
energy seems reasonable before trying again.
Variable ci has value -2147483648. It should have been within [ 0 .. 4913 ]
My mdp file is pretty similar to the one provided in the reverse transformation tutorial. Please help me in this regard.
I was reverse transforming my CG system to AA. My system contains lipids. I am following the reverse transformation tutorial. When I am doing simulated annealing, I am getting the following error.
Warning: 1-4 interaction between 1832 and 1853 at distance 1.219 which is larger than the 1-4 table size 1.200 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
step 0
Program mdrun, VERSION 3.3.1
Source code file: nsgrid.c, line: 226
Range checking error:
Explanation: During neighborsearching, we assign each particle to a grid
based on its coordinates. If your system contains collisions or parameter
errors that give particles very high velocities you might end up with some
coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
put these on a grid, so this is usually where we detect those errors.
Make sure your system is properly energy-minimized and that the potential
energy seems reasonable before trying again.
Variable ci has value -2147483648. It should have been within [ 0 .. 4913 ]
My mdp file is pretty similar to the one provided in the reverse transformation tutorial. Please help me in this regard.
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- djurre
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11 years 8 hours ago #1550
by djurre
Replied by djurre on topic Simulated annealing error
There is something in your system that is instable and makes it explode. From the current information I can't tell what it is. Try the usual tricks to make it more stable.
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