Dear Amber users,
I have been trying to run the simplest QM that contains sodium in Amber: a system with just 1 Na+ atom. With PM6 this seems to work fine for just a couple of frames (femtoseconds), but with DFTB3 I cannot seem to make it work. I have tried with the following Amber versions: amber/20, amber/20_new, amber/20-cuda_new, amber/20-cuda, amber/20-quick-cuda, amber/test-20, amber/18, and amber/18-cuda. For all these Amber versions I get the same error (this specific one is for amber/20):
-------------------------------------------------------
Amber 20 SANDER 2020
-------------------------------------------------------
| Run on 03/21/2022 at 14:29:40
| Executable path: /appl/soft/chem/amber/20-gcc/bin/sander.MPI
| Working directory: /scratch/project_2002241/mayorgad/micelle66_runs/M67_moreH2O/WATER_ENERGIES/DFTB_TESTS
| Hostname: r02c02.bullx
[-O]verwriting output
File Assignments:
| MDIN: 1NaQM.in
| MDOUT: 1NaQM.out
|INPCRD: 1NaCoord.rst
| PARM: 1Na.prmtop
|RESTRT: 1NaQM.rst
| REFC: refc
| MDVEL: mdvel
| MDFRC: mdfrc
| MDEN: mden
| MDCRD: 1NaQM.mdcrd
|MDINFO: mdinfo
| MTMD: mtmd
|INPDIP: inpdip
|RSTDIP: rstdip
|INPTRA: inptraj
| REMLOG: rem.log
| REMTYPE: rem.type
| REMSTRIP:
| SAVEENE: saveene
|CLUSTERINF: cluster.info
| RESERVOIR: reserv/frame
| REMDDIM:
Here is the input file:
Acet, meoh: 300ps MD, No constraints, now with constant volume, keeping thermal bath
&cntrl
imin = 0, ! do MD (no minimization)
irest = 0, ! restart calculation
ntx = 1, ! no vel
ntb = 0, ! NON-PERIODIC
ntp = 0, ! 0) No pressure scaling 1) constant pressure dynamics, isotropic position scaling
tautp = 10.0, ! Time constant, in ps, for heat bath coupling for the system, if ntt = 1.
cut = 9.0, ! force cutoff boundary
ntr = 0, ! NO Position restraints
NTC = 1, ! SHAKE not performed
NTF = 1, ! complete interaction is calculated (default)
jfastw=4 ! No shake mask
tempi = 295.15, ! intial temp
temp0 = 295.15, ! goal, final temp
ntt = 1, ! Use Langevin dynamics using the weak-coupling algorithm, see tautp
ig=-1, ! random seed will be based on the current date and time
nstlim = 3,! the number of MD steps
dt = 0.001, ! time step (ps)
ntpr = 1, ! results prited every ntpr
ntwx = 1, ! coordinate file printed every ntwx
ntwr = 1, ! restart file printed every ntwr
ifqnt = 1, ! Flag for QM/MM run
/
&qmmm
qmmask=':Na+', ! Residue 1 is QM treated (the Oxalate acid)
qmcharge =1, ! Charge of QM region
qm_theory ='DFTB3',! Use PM3 Hamiltonian (default)
qm_ewald=0, ! Use Ewald type treatment for long range Electrostatics
qm_pme=1 ! Particle Mesh Ewald method
/
--------------------------------------------------------------------------------
1. RESOURCE USE:
--------------------------------------------------------------------------------
| Flags: MPI
| NONPERIODIC ntb=0 and igb=0: Setting up nonperiodic simulation
|Largest sphere to fit in unit cell has radius = 50.038
| New format PARM file being parsed.
| Version = 1.000 Date = 03/21/22 Time = 13:59:55
NATOM = 1 NTYPES = 1 NBONH = 0 MBONA = 0
NTHETH = 0 MTHETA = 0 NPHIH = 0 MPHIA = 0
NHPARM = 0 NPARM = 0 NNB = 1 NRES = 1
NBONA = 0 NTHETA = 0 NPHIA = 0 NUMBND = 0
NUMANG = 0 NPTRA = 0 NATYP = 7 NPHB = 0
IFBOX = 0 NMXRS = 1 IFCAP = 0 NEXTRA = 0
NCOPY = 0
| Memory Use Allocated
| Real 502243
| Hollerith 6
| Integer 20023
| Max Pairs 0
| nblistReal 12
| nblist Int 2544473
| Total 13941 kbytes
| 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 :Na+; matches 1 atoms
Note: ig = -1. Setting random seed to 373151 based on wallclock time in microseconds
and disabling the synchronization of random numbers between tasks
to improve performance.
--------------------------------------------------------------------------------
2. CONTROL DATA FOR THE RUN
--------------------------------------------------------------------------------
Molden
General flags:
imin = 0, nmropt = 0
Nature and format of input:
ntx = 1, irest = 0, ntrx = 1
Nature and format of output:
ntxo = 2, ntpr = 1, ntrx = 1, ntwr = 1
iwrap = 0, ntwx = 1, ntwv = 0, ntwe = 0
ioutfm = 1, ntwprt = 0, idecomp = 0, rbornstat= 0
Potential function:
ntf = 1, ntb = 0, igb = 0, nsnb = 25
ipol = 0, gbsa = 0, iesp = 0
dielc = 1.00000, cut = 9.00000, intdiel = 1.00000
Frozen or restrained atoms:
ibelly = 0, ntr = 0
Molecular dynamics:
nstlim = 3, nscm = 1000, nrespa = 1
t = 0.00000, dt = 0.00100, vlimit = 20.00000
Berendsen (weak-coupling) temperature regulation:
temp0 = 295.15000, tempi = 295.15000, tautp = 10.00000
QMMM options:
ifqnt = True nquant = 1
qmgb = 0 qmcharge = 1 adjust_q = 2
spin = 1 qmcut = 9.0000 qmshake = 1
qmmm_int = 1
lnk_atomic_no = 1 lnk_dis = 1.0900 lnk_method = 1
qm_theory = DFTB verbosity = 0
qmqmdx = Analytical
tight_p_conv = False (converge density to 0.05xSqrt[SCFCRT])
scfconv = 0.100E-07 itrmax = 1000
printcharges = False printdipole = False peptide_corr = False
qmmmrij_incore = False
qmqm_erep_incore = False
pseudo_diag = False
diag_routine = 0
qm_ewald = 0 qm_pme = False
| MPI Timing options:
| profile_mpi = 0
| INFO: Old style inpcrd file read
--------------------------------------------------------------------------------
3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------
MOLECULE
begin time read from input coords = 0.000 ps
Number of triangulated 3-point waters found: 0
| Atom division among processors:
| 0 1
|QMMM: Running QMMM calculation in parallel mode on 1 threads.
|QMMM: All atom division among threads:
|QMMM: Start End Count
|QMMM: Thread( 0): 1-> 1 ( 1)
|QMMM: Quantum atom + link atom division among threads:
|QMMM: Start End Count
|QMMM: Thread( 0): 1-> 1 ( 1)
Sum of charges from parm topology file = 1.00000000
| Running AMBER/MPI version on 1 nodes
| # of SOLUTE degrees of freedom (RNDFP): 3.
| # of SOLVENT degrees of freedom (RNDFS): 0.
| QMSHAKE_NOSHAKEMASK_OVERLAP = 0
| NDFMIN = 0. NUM_NOSHAKE = 0 CORRECTED RNDFP = 0.
| TOTAL # of degrees of freedom (RNDF) = 0.
---------------------------------------------------
eedmeth=4: Setting switch to one everywhere
---------------------------------------------------
| Local SIZE OF NONBOND LIST = 0
| TOTAL SIZE OF NONBOND LIST = 0
QMMM: Link Atom Information
QMMM: ------------------------------------------------------------------------
QMMM: nlink = 0
QMMM: ------------------------------------------------------------------------
QMMM: QM Region Cartesian Coordinates (*=link atom)
QMMM: QM_NO. MM_NO. ATOM X Y Z
QMMM: 1 1 Na 40.0760 52.2980 62.3450
--------------------------------------------------------------------------------
3.1 QM CALCULATION INFO
--------------------------------------------------------------------------------
| QMMM: Citation for AMBER QMMM Run:
| QMMM: R.C. Walker, M.F. Crowley and D.A. Case, J. COMP. CHEM. 29:1019, 2008
| QMMM: DFTB Calculation - Additional citation for AMBER DFTB QMMM Run:
| QMMM: Seabra, G.M., Walker, R.C. et al., J. PHYS. CHEM. A., 111, 5655, (2007)
| QMMM: DFTB3 - Additional citation to follow. Implementation by:
| QMMM: A.W. Goetz
| QMMM:
| QMMM: DFTB3 method citation:
| QMMM: M. Gaus, Q. Cui, M. Elstner, J. CHEM. THEORY COMPUT. 7, 931 (2011)
| QMMM:
| QMMM: DFTB3 dispersion correction [D3(BJ)] and halogen correction not available.
| QMMM: Please cite also the appropriate references for the DFTB parameters
| QMMM: that you are using (see the manual and www.dftb.org).
QMMM: SINGLET STATE CALCULATION
QMMM: RHF CALCULATION, NO. OF DOUBLY OCCUPIED LEVELS = 0
DFTB: Number of atom types = 1
Parameter files:
TYP (AT) TYP (AT) SK integral FILE
| 1 1 (Na) 1 (Na) /appl/soft/chem/amber/20-gcc/dat/slko/3ob-3-1/Na-Na.skf
SANDER BOMB in subroutine qm2_dftb_get_dftb3_parameters
Hubbard derivative dU/dq not found.
Element Na not supported.
Seems that Na is not supported, but it should be, since the file Na-Na.skf is in 3ob-3-1 as seen in the output message. With a system of water and organic molecules DFTB3 works just fine, but when Na+ is added this error message just pops up. Is there any viable solution? Thanks.
BR,
Pau
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Received on Mon Mar 21 2022 - 06:00:03 PDT
