Dear all,
I am doing the constant pH simulations of Amber, for I can change the
pH of system during the MD simulation. But I have met some problems
which trouble me a lot.
My system includes protein, ligand and three Mg2+ ions. When heating
and equilibrating the system, which atoms should I restrain, all of
them? After heat and equilibration, the conformation changed a lot
and the RMSD increased to 10 above.At the first step in product MD,
temperture increased to about 362K, I don't know why. At 480ps, the
temperature turned to 400 above. And the simulation stopped at about
500ps, the error information is as followed:
vlimit exceeded for step 259584; vmax = 1139.7184
Coordinate resetting (SHAKE) cannot be accomplished,
deviation is too large
NITER, NIT, LL, I and J are : 0 2 10 1 3
Note: This is usually a symptom of some deeper
problem with the energetics of the system.
Who can tell me what causes this and what should I modify about it?
Thanks a lot!!
Wen-ting Chu
Jilin university, China
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Received on Fri Nov 19 2010 - 00:00:03 PST
