Dear Amber members:
I have meet several questions about Amber adaptive QM/MM MD. I am doing a QM/MM umbrella sampling to scan the potential energy surface and the QM theory for A region is DFTB3. I found out that several water molecules fluctuate very fast and the DFTB3 calculations could not achieve convergent result after 50 time steps,then the sander bombed¡£Before each QM/MM calculations, I have run several picoseconds MM MD to make sure the structure normal. My input file md_equil.in is shown as follows:
50 ps equilibration for Zn and COO
&cntrl
imin = 0, ntx = 1, irest = 0,
ntpr = 1, ntwr = 1, ntwx = 1,
ntf = 1, ntc = 1, cut = 999.0,
ntb = 0, nstlim = 10000, dt = 0.001,
tempi=300.0, temp0 = 300.0, ntt = 6,
gamma_ln = 1.0,igb=0,
nmropt = 1, ioutfm=0,
ivcap=0,
fcap=20.0,
ntr=1,restraintmask='.5 ',restraint_wt=300.0,
ifqnt=1
&end
&qmmm
qmmask=':1,2',# the Zinc ion and a COO-
qmcharge=1
spin=1
vsolv=2
adjust_q=0
qmcut=8.0
qm_theory='dftb3'
&end
&vsolv
nearest_qm_solvent=10
qm_center_atom_id=5 # atom index of CD atom in COO-
&end
&adqmmm
n_partition =10
verbosity=1
print_qm_coords=1
/
&wt
type='END',
&end
DISANG=disZNC.in
And my prmtop file and initial coordinate file are listed in accessory. To solve this problem, I have test different values of n_partition parameter, but the results are almost the same¡£
Could you help me? It's really my honor to receive any letter from you£¬thank you ¡£
Best wishes for you!
Mingyuan
2017.12.18
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- application/octet-stream attachment: disZNC.in
Received on Mon Dec 18 2017 - 09:00:02 PST
