[gmx-users] mdrun error

[amitbehra at chemeng.iisc.ernet.in]

Hello,
After equilibrating my system for 100 ns( during which there was restraint
on the protein letting the lipids to equilibrate), when I am trying to run
my unrestrained run I am getting the following errors:
1. "bonds that rotated more than 30 degree"
2. "1 particles communicated to PME rank 0 are more than 2/3 times the
cut-off out of the domain decomposition cell of their charge group in
dimension x"
3. "Listed nonbonded interaction between particles 71916 and 71920
at distance 5.535 which is larger than the table limit 2.215 nm."

What might be the reason for this error. I thought 100ns is enough for
equilibration.

Thanks,
Amit Behera
Research Scholar,
IISc.

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