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Problem with reverse transformation
- lihie
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12 years 2 months ago #916
by lihie
Problem with reverse transformation was created by lihie
Hello,
I'm trying to learn the reverse transformation protocol using the tutorial files, but when I got to the SA run I'm receiving the following error:
Warning: 1-4 interaction between 1768 and 1789 at distance 1.268 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.
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode -1.
NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
I'm doing exactly what is written in the tutorial.
Can anyone help me?
Thank you,
Lihie
I'm trying to learn the reverse transformation protocol using the tutorial files, but when I got to the SA run I'm receiving the following error:
Warning: 1-4 interaction between 1768 and 1789 at distance 1.268 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.
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode -1.
NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
I'm doing exactly what is written in the tutorial.
Can anyone help me?
Thank you,
Lihie
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