Zuzana Benkova wrote:
I have run an NVE simulation of decamer of glycin first with PBC
(coulombtype=Cut-off) and later without PBC (coulombtype=PME).
You can't have a non-periodic system with PME.
The
gen-temp was set to 300K with option gen-vel=yes. The temperature start
to raise during simulation and finaly the following messages appeared in
log file
Shake did not converge in 1000 steps
i mi j mj before after should be
66 14.01 67 1.01 0.10100 0.10318 0.10100
Constraint error in algorithm Shake at step 980454
Wrote pdb files with previous and current coordinates
How can I cope with this?
We can't tell, because the above description is not self-consistent.
In any case you haven't defined your topology, or minimized your
structure or equilibrated properly. Then some bad structural element is
causing a region to have too much energy which is breaking structures.
Search the mailing list archives for suggested equilibration regimes, or
read relevant literature examples, or do tutorial material.
Mark
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