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.
The structure has been successfully quantum minimised (GMAX=40, RMS=1.8) prior to the MD; treating only a few residues, the ligand, the Mg ion and the water molecules quantum dynamically.
I tried to run the molecular dynamics simulation treating quantum dynamically the same region of the system as during the minimisation but got an error message saying “vlimit exceeded for step..”. Neither adding shake options, nor reducing the time step helped and, when the simulation was achieved, the temperature and the total energy were extremely high. Here is the input file:
100K temp QMMMMD
&cntrl
imin=0,
ntb=0,
igb=1,
cut=12.0,
tempi=0.0, temp0=100.0,
ntc=2, ntf=2,
ntt=3, gamma_ln=2.0,
nstlim=1000, dt=0.0005,
ntpr=1, ntwx=1,ifqnt=1,
ntr=1,
restraintmask = ':170,185,.CA,C,N',
restraint_wt = 5.0
/
&qmmm
qmmask=':59,61,168,169,186-188',
qmcharge=-2,
qm_theory='PM3',
qmshake=0,
qmcut=12.0,
/
I run then the same molecular dynamics simulation without the quantum treatment. It was successfully achieved but one of the water molecules had slipped away from the active site.. Only when restraining it with a force of 20 kcal/mol.A°2 it would remain in it.
Here is the input file of the simulation when a water molecule "escapes":
Heating 0 to 300K MD
&cntrl
imin=0,
ntb=0,
igb=1,
cut=12.0,
tempi=0.0, temp0=300.0,
ntt=3, gamma_ln=2.0,
nstlim=10000, dt=0.001,
ntpr=100, ntwx=100,
ntr=1,
restraintmask = ':170,185,.CA,C,N',
restraint_wt=10.0,
/
So I wander:
_How a water molecule could go so far away?
_Could the “special routines” of shake used for water molecules be the reason of the “vlimit exceeded” when they are treated quantum dynamically?
Has anyone a clue of what I should add/change/remove?
Thank you,
Ruth
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Received on Tue Sep 15 2015 - 09:30:03 PDT
