Dear AMBER users,
I am performing MD simulation of a *protein–ligand–membrane system* in
AMBER and encountering instability during the equilibration stage.
Workflow followed:
1.
System minimization
2.
Two-step heating process
3.
Equilibration with gradual removal of restraints:
-
first lipid dihedral restraints were gradually reduced
-
then lipid positional restraints were gradually reduced
The minimization and heating stages completed successfully. Some initial
equilibration steps also run successfully, but after a few equilibration
stages I start getting the following error:
*vlimit exceeded for step 38; vmax = 22.9627
vlimit exceeded for step 39; vmax = 83.0116**
Coordinate resetting cannot be accomplished,
deviation is too large
iter_cnt, my_bond_idx, i and j are : 4 4273 7888 7890*
Additional observations:
-
Sometimes the simulation continues for a few steps when I switch from
GPU to CPU execution.
-
However, later equilibration stages fail again with the same error.
-
The error occurs both when changing restraints and even when running
subsequent equilibration steps without modifying restraint settings.
I would appreciate any suggestions regarding:
-
Possible causes of this instability
-
Best practices for equilibration of membrane systems with gradual
restraint release
-
Whether the issue could be related to restart/reference handling between
equilibration stages
-
Recommended approaches to systematically troubleshoot and stabilize this
protein–ligand–membrane equilibration process
*I have also attached a .txt file containing the relevant section of the
.mdout file showing the complete error message for reference.*
I would be very grateful for any advice or insights from experienced AMBER
users.
Thank you very much for your help.
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Received on Wed May 20 2026 - 23:30:02 PDT
