[gmx-users] removing a water molecule

Ragothaman Yennamalli ymr79in at yahoo.co.in
Mon May 28 08:36:08 CEST 2007

Dear all,
I am running a MD simulation, which stops after 6ns
run with an error saying:

t = 6825.932 ps: Water molecule starting at atom 19637
can not be settled.
Check for bad contacts and/or reduce the
timestep.Wrote pdb files with previous and current

How does one proceed from here? Is removing the single
water molecule a solution? In that case wouldn't there
be a conflict between the number of atoms of previous
trr file and the new one being made?

Thanks in advance,

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