Hi Stregone,
Have you tried this with water before? There are corresponding tests in $AMBERHOME/test/qmmm2/adqmmm_h2o-box, similar to what you are trying to do. I only tested water but the adaptive QM/MM implementation should work with any residue.
At first glance, your input looks OK to me. If you send me (off-list) your input files, I can have a look at what is going wrong.
Thanks,
Andy
—
Dr. Andreas W. Goetz
Assistant Project Scientist
San Diego Supercomputer Center
Tel: +1-858-822-4771
Email: agoetz.sdsc.edu
Web: www.awgoetz.de
> On Sep 19, 2016, at 5:12 AM, Stregone <stregone.protonmail.com> wrote:
>
> 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 - 21:00:02 PDT
