Good day! Amber Community,
I do try to make work an adaptive qm/mm NVT simulation,
So far I am able to run the qmm/mm NVT simulation without problem,
however when I start to use the keywords for the adaptive part, AMBER 14
gave me a error in the out file.
Here is the information from the out file, it includes the keywords used.
NVT simulation
&cntrl
imin = 0, ! do MD (no minimization)
irest = 0, ntx =1,
ntb = 1, cut = 10.0,
ntt = 3, gamma_ln = 5.0, g = -1,
tempi = 298.15, temp0 = 298.15,
nstlim = 2800000, dt = 0.0005,
ntpr = 200, ntwr = 200, ntwv = 200, ntwx = 200,
iwrap = 1, ifqnt=1,
/
&qmmm
qmmask='.1-12', qmcharge=0, qm_theory='PM6',
qmshake=0, qm_ewald=1, qm_pme=1, printdipole = 2,
verbosity =0, scfconv = 0.100E-09,
tight_p_conv = 1, adjust_q = 0,
vsolv = 3, ! adQMMM with fixed RA and RT
qmmm_switch=1, r_switch_hi=11, r_switch_lo=9, writepdb=1,
/
&ewald
skinnb = 2.0, dsum_tol = 0.000001,
/
&vsolv
verbosity = 1, debug = 0,
nearest_qm_solvent = 2, ! solvent in active region
nearest_qm_solvent_resname = 'BBZ', ! solvent resname
nearest_qm_solvent_fq = 1, ! every step
nearest_qm_solvent_center_id = 0, ! number of atom in solvent residue defining solvent center
qm_center_atom_id = 6, ! atom defining QM center
/
&adqmmm
!n_partition = 6, ! (n-1) molecules in T region
RA = 3.50, RT = 4.15,
calc_wbk = 2, ! calculate energy correction
verbosity = 3, print_qm_coords = 0,
/
--------------------------------------------------------------------------------
1. RESOURCE USE:
--------------------------------------------------------------------------------
| Flags: MPI
getting new box info from bottom of inpcrd
| INFO: Old style inpcrd file read
| peek_ewald_inpcrd: Box info found
|Largest sphere to fit in unit cell has radius = 35.590
| New format PARM file being parsed.
| Version = 1.000 Date = 06/11/16 Time = 12:19:12
NATOM = 30204 NTYPES = 3 NBONH = 12585 MBONA = 17619
NTHETH = 25170 MTHETA = 20136 NPHIH = 40272 MPHIA = 20136
NHPARM = 0 NPARM = 0 NNB = 133401 NRES = 2517
NBONA = 17619 NTHETA = 20136 NPHIA = 20136 NUMBND = 3
NUMANG = 3 NPTRA = 1 NATYP = 3 NPHB = 0
IFBOX = 1 NMXRS = 12 IFCAP = 0 NEXTRA = 0
NCOPY = 0
| Note: 1-4 EEL scale factors are being read from the topology file.
| Note: 1-4 VDW scale factors are being read from the topology file.
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals
LOADING THE QUANTUM ATOMS AS GROUPS
Mask .1-12; matches 12 atoms
RESIDUE 1 IS IN QM REGION
RESIDUE 1 IS IN QM REGION
QMMM: Variable QM Solvent Region is Active
QMMM: ------------------------------------------------------
QMMM: Residue name of solvent molecules : BBZ
QMMM: Atoms per solvent molecule : 12
QMMM: Total number of solvent molecules to consider : 2516
QMMM: Atoms in fixed QM region : 12
QMMM: Atoms in variable QM solvent region : ******
QMMM: Total atoms in QM region : ******
QMMM: QM Solvent region update frequency (steps) : 1
QMMM: ------------------------------------------------------
PARAMETER RANGE CHECKING:
parameter QMMM: (number of quantum atoms) has value -393156
This is outside the legal range
Lower limit: 1 Upper limit: 10000
The limits may be adjustable; search in the .h files
I reckon that the error is on the solvent resname. I mean adQM/MM is designed
for simulations with water molecules as solvent. In my case I do use other molecule,
a organic solvent, however I have not found anywhere that adQM/MM is explicitly
used with water molecules.
I will appreciate any help.
Thanks in advance.
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Received on Mon Sep 19 2016 - 05:30:04 PDT
