Hi Amber community,
I’m running a molecular dynamics simulation of a protein with its ligand and an Mg +2 ion in implicit solvent although there are tree water molecules in the active region as they are necessary for the reaction to proceed.
I’m modeling quantum mechanically (QMMM) a few residues with the PME method, as well as the Mg ion, the tree water molecules and the ligand (which contains phosphates).
The structure has been successfully quantum minimised prior to the MD/QMMM run and in the later (which, for now, nstlim=1000 only) the initial temperature is 0°K and the final one is 100°K (tempi=0.0, temp0=100.0)
I started with dt=0.002 and no shake options. I got an error message which said: “vlimit exceeded for step..”
and also: "This is usually a a symptom of some deeper problem with the energetics of the system”
Searching on the amber archives, I found that I should decrease dt and add some shake options (ntc=2 and nff=2) in the input file. Yet, these changes (dt=0.001 and even dt=0.0005) didn’t help. Well, by diminishing dt without adding the shake options, the simulation reaches the final step but the temperature and the total energy are incredibly (unrealistically) high.
Has anyone a clue of what I should add/change/remove??
Thank you,
Ruth
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Sep 11 2015 - 08:00:05 PDT
