API not compatible with free energy calculation #392
Description
Hi All,
I have recently been running QM/MM/TI with Quick, but sadly, it does not support API. Please see the code and error output below:
The command used: mpirun -n 2 sander.quick.cuda.MPI -ng 2 -groupfile mm2qmmm.0.00.groupfile
mm2qmmm.0.00.groupfile:
-O -p ../../../common/vac.parm7 -i mm.0.00.mdin -o mm.0.00.mdout -c init.0.00.rst7 -r mm.0.00.rst7 -x mm.0.00.nc -inf mm.0.00.mdinfo
-O -p ../../../common/vac.parm7 -i qm.0.00.mdin -o qm.0.00.mdout -c init.0.00.rst7 -r qm.0.00.rst7 -x qm.0.00.nc -inf qm.0.00.mdinfo
qm.0.00.mdin and mm.0.00.mdin (these two files only differ slightly)
Equilibrium TI analysis
&cntrl
! IO =======================================
irest = 1 ! 0 = start, 1 = restart
ntx = 5 ! 1 = start, 5 = restart
ntxo = 1 ! read/write rst as formatted file
iwrap = 1 ! wrap crds to unit cell
ioutfm = 1 ! write mdcrd as netcdf
ntpr = 10 ! mdout print freq
ntwx = 500 ! mdcrd print freq
ntwr = 500 ! rst print freq
ntwv = 0
! DYNAMICS =================================
! - - ATTN: the 2 fs timestep only works if the parm7 was modified with hydrogen mass repartitioning - -
imin = 0 ! Run dynamics
dt = 0.0005 ! ps/step
nstlim = 5000 ! number of time steps (per simulation)
ntb = 1 ! 1=periodic box
! TEMPERATURE ==============================
temp0 = 298 ! target temp
gamma_ln = 5.0 ! Langevin collision freq
ntt = 3 ! thermostat (3=Langevin)
! Use middle scheme rather than the default leapfrog integrator
! so the middle scheme people dont complain. Supposedly its more stable.
! ntt = 0
! ischeme = 1 ! middle scheme
!ithermostat = 1 ! Langevin
!therm_par = 5.0 ! Langevin collision freq
! PRESSURE ================================
ntp = 0 !0=off 1=isotropic scaling
! taup = 2.0 ! pressure relaxation time
! pres0 = 1.013 ! pressure (bar), 1.013 bar/atm
! barostat = 1 ! barostat (1=Berendsen, 2=MC)
! SHAKE ====================================
ntc = 2 ! 1=no shake, 2=HX constrained, 3=all constrained
ntf = 1 ! 1=cpt all bond E, 2=ignore HX bond E, 3=ignore all bond E
noshakemask=':1'
! MISC =====================================
cut = 10
ig = -1
ifqnt = 1 !!!!!!!!!!! if mm, this value is set to zero
! TI =======================================
icfe = 1 ! interpret groupfile as being a FE simulation; first group is MM, second is QM/MM
clambda = 0.00 ! Manually set lambda. 0=MM, 1=QM/MM
ifmbar = 1 ! print the lam=0 and lam=1 energies
bar_intervall = 10
bar_l_min = 0
bar_l_max = 1
bar_l_incr = 1
dynlmb = 0
ntave = 0
/
&ewald
dsum_tol = 1.e-6
/
&qmmm
qm_theory = 'quick',
qmmask = ':1',
qmmm_int = 1,
qm_ewald = 0,
qmshake = 0,
/
&quick
method = 'B3LYP',
basis = 'def2-svp',
/
vac.parm7
%VERSION VERSION_STAMP = V0001.000 DATE = 11/22/24 11:55:56
%FLAG TITLE
%FORMAT(20a4)
default_name
%FLAG POINTERS
%FORMAT(10I8)
5 2 4 0 6 0 0 0 0 0
11 1 0 0 0 1 1 0 2 0
0 0 0 0 0 0 0 1 5 0
0
%FLAG ATOM_NAME
%FORMAT(20a4)
C1 H1 H2 H3 H4
%FLAG CHARGE
%FORMAT(5E16.8)
-8.23108580E+00 2.05777145E+00 2.05777145E+00 2.05777145E+00 2.05777145E+00
%FLAG ATOMIC_NUMBER
%FORMAT(10I8)
6 1 1 1 1
%FLAG MASS
%FORMAT(5E16.8)
1.20100000E+01 1.00800000E+00 1.00800000E+00 1.00800000E+00 1.00800000E+00
%FLAG ATOM_TYPE_INDEX
%FORMAT(10I8)
1 2 2 2 2
%FLAG NUMBER_EXCLUDED_ATOMS
%FORMAT(10I8)
4 3 2 1 1
%FLAG NONBONDED_PARM_INDEX
%FORMAT(10I8)
1 2 2 3
%FLAG RESIDUE_LABEL
%FORMAT(20a4)
MET
%FLAG RESIDUE_POINTER
%FORMAT(10I8)
1
%FLAG BOND_FORCE_CONSTANT
%FORMAT(5E16.8)
3.45250000E+02
%FLAG BOND_EQUIL_VALUE
%FORMAT(5E16.8)
1.09620000E+00
%FLAG ANGLE_FORCE_CONSTANT
%FORMAT(5E16.8)
3.58000000E+01
%FLAG ANGLE_EQUIL_VALUE
%FORMAT(5E16.8)
1.88024401E+00
%FLAG DIHEDRAL_FORCE_CONSTANT
%FORMAT(5E16.8)
%FLAG DIHEDRAL_PERIODICITY
%FORMAT(5E16.8)
%FLAG DIHEDRAL_PHASE
%FORMAT(5E16.8)
%FLAG SCEE_SCALE_FACTOR
%FORMAT(5E16.8)
%FLAG SCNB_SCALE_FACTOR
%FORMAT(5E16.8)
%FLAG SOLTY
%FORMAT(5E16.8)
0.00000000E+00 0.00000000E+00
%FLAG LENNARD_JONES_ACOEF
%FORMAT(5E16.8)
1.02073671E+06 1.00235148E+05 7.94617769E+03
%FLAG LENNARD_JONES_BCOEF
%FORMAT(5E16.8)
6.63431737E+02 1.37787728E+02 2.57122925E+01
%FLAG BONDS_INC_HYDROGEN
%FORMAT(10I8)
0 3 1 0 6 1 0 9 1 0
12 1
%FLAG BONDS_WITHOUT_HYDROGEN
%FORMAT(10I8)
%FLAG ANGLES_INC_HYDROGEN
%FORMAT(10I8)
9 0 12 1 6 0 9 1 6 0
12 1 3 0 6 1 3 0 9 1
3 0 12 1
%FLAG ANGLES_WITHOUT_HYDROGEN
%FORMAT(10I8)
%FLAG DIHEDRALS_INC_HYDROGEN
%FORMAT(10I8)
%FLAG DIHEDRALS_WITHOUT_HYDROGEN
%FORMAT(10I8)
%FLAG EXCLUDED_ATOMS_LIST
%FORMAT(10I8)
2 3 4 5 3 4 5 4 5 5
0
%FLAG HBOND_ACOEF
%FORMAT(5E16.8)
%FLAG HBOND_BCOEF
%FORMAT(5E16.8)
%FLAG HBCUT
%FORMAT(5E16.8)
%FLAG AMBER_ATOM_TYPE
%FORMAT(20a4)
c3 hc hc hc hc
%FLAG TREE_CHAIN_CLASSIFICATION
%FORMAT(20a4)
BLA BLA BLA BLA BLA
%FLAG JOIN_ARRAY
%FORMAT(10I8)
0 0 0 0 0
%FLAG IROTAT
%FORMAT(10I8)
0 0 0 0 0
%FLAG SOLVENT_POINTERS
%FORMAT(3I8)
1 1 2
%FLAG ATOMS_PER_MOLECULE
%FORMAT(10I8)
5
%FLAG BOX_DIMENSIONS
%FORMAT(5E16.8)
9.00000000E+01 4.80000000E+01 4.80000000E+01 4.80000000E+01
%FLAG RADIUS_SET
%FORMAT(1a80)
modified Bondi radii (mbondi)
%FLAG RADII
%FORMAT(5E16.8)
1.70000000E+00 1.30000000E+00 1.30000000E+00 1.30000000E+00 1.30000000E+00
%FLAG SCREEN
%FORMAT(5E16.8)
7.20000000E-01 8.50000000E-01 8.50000000E-01 8.50000000E-01 8.50000000E-01
%FLAG IPOL
%FORMAT(1I8)
0
init.0.00.rst7
Please find the dropbox link. https://www.dropbox.com/scl/fi/q6bbwrsnz8p18n3awg9ga/init.0.00.rst7?rlkey=hmw1ux3kg0b9plyzmooqlr2xi&st=ykvbxy4m&dl=0
Error: The job keeps stuck at this stage of the output files: Looks like some memory competition happened.
--------------------------------------------------------------------------------
4. RESULTS
--------------------------------------------------------------------------------
| # of SOLUTE degrees of freedom (RNDFP): 11.
| # of SOLVENT degrees of freedom (RNDFS): 0.
| NDFMIN = 15. NUM_NOSHAKE = 4 CORRECTED RNDFP = 15.
| TOTAL # of degrees of freedom (RNDF) = 15.
---------------------------------------------------
APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION
using 5000.0 points per unit in tabled values
TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff
| CHECK switch(x): max rel err = 0.2738E-14 at 2.422500
| CHECK d/dx switch(x): max rel err = 0.8987E-11 at 2.875760
---------------------------------------------------
| Local SIZE OF NONBOND LIST = 0
| TOTAL SIZE OF NONBOND LIST = 0