Hi,
I'm trying to resolve some issues with the minimization that is leading to vlimit exceeding and more issues later in my simulation. It is a solution with some ions and a water solvent. I'm wondering if this message after I set up the initial coordinates through tleap has anything to do with it. I have multiple ions, nitrate, and water molecules but this comes up.
Thanks for any help.
Incorporating Non-Bonded adjustments.
Not Marking per-residue atom chain types.
Marking per-residue atom chain types.
(Residues lacking connect0/connect1 -
these don't have chain types marked:
res total affected
WAT 550
itr 1
)
This occurs in the heating equilibration of the simulation
Here is the input file:
Heating of 1M NaNO3 STAGE 1
&cntrl
imin=0, irest=0, ntx=1,
nstlim=4000000, dt=0.0005,
cut=4.0,
ntf=2,ntc=2,
ntt=3, gamma_ln=1.0,
tempi=0.0, temp0=100.0,
ntpr=50, ntwx=50,
ntb=1,
iwrap=1, ipol=1, ig=-1
/
--------------------------------------------------------------------------------
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 = 29.901
| New format PARM file being parsed.
| Version = 1.000 Date = 09/13/15 Time = 17:27:04
NATOM = 1657 NTYPES = 6 NBONH = 1100 MBONA = 3
NTHETH = 0 MTHETA = 3 NPHIH = 0 MPHIA = 0
NHPARM = 0 NPARM = 0 NNB = 2210 NRES = 554
NBONA = 3 NTHETA = 3 NPHIA = 0 NUMBND = 4
NUMANG = 3 NPTRA = 0 NATYP = 9 NPHB = 0
IFBOX = 1 NMXRS = 4 IFCAP = 0 NEXTRA = 0
NCOPY = 0
| Memory Use Allocated
| Real 226980
| Hollerith 5527
| Integer 54849
| Max Pairs 14913
| nblistReal 19884
| nblist Int 1569697
| Total 8354 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
BOX TYPE: RECTILINEAR
Note: ig = -1. Setting random seed to 704524 based on wallclock time in microseconds
and disabling the synchronization of random numbers between tasks
to improve performance.
--------------------------------------------------------------------------------
2. CONTROL DATA FOR THE RUN
--------------------------------------------------------------------------------
default_name
General flags:
imin = 0, nmropt = 0
Nature and format of input:
ntx = 1, irest = 0, ntrx = 1
Nature and format of output:
ntxo = 1, ntpr = 50, ntrx = 1, ntwr = 500
iwrap = 1, ntwx = 50, ntwv = 0, ntwe = 0
ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0
Potential function:
ntf = 2, ntb = 1, igb = 0, nsnb = 25
ipol = 1, gbsa = 0, iesp = 0
dielc = 1.00000, cut = 4.00000, intdiel = 1.00000
Frozen or restrained atoms:
ibelly = 0, ntr = 0
Molecular dynamics:
nstlim = 4000000, nscm = 1000, nrespa = 1
t = 0.00000, dt = 0.00050, vlimit = 20.00000
Langevin dynamics temperature regulation:
ig = 704524
temp0 = 100.00000, tempi = 0.00000, gamma_ln= 1.00000
SHAKE:
ntc = 2, jfastw = 0
tol = 0.00001
Polarizable options:
indmeth = 3, maxiter = 20, irstdip = 0, scaldip = 1
diptau = 11.00000, dipmass = 0.33000
Ewald parameters:
verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1
vdwmeth = 1, eedmeth = 1, netfrc = 1
Box X = 59.801 Box Y = 60.656 Box Z = 60.193
Alpha = 90.000 Beta = 90.000 Gamma = 90.000
NFFT1 = 60 NFFT2 = 60 NFFT3 = 60
Cutoff= 4.000 Tol =0.100E-04
Ewald Coefficient = 0.72611
Interpolation order = 4
| MPI Timing options:
| profile_mpi = 0
--------------------------------------------------------------------------------
3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------
defa
begin time read from input coords = 0.000 ps
Number of triangulated 3-point waters found: 0
| Atom division among processors:
| 0 208 415 622 829 1036 1243 1450
| 1657
Sum of charges from parm topology file = -0.00000000
Forcing neutrality...
| Running AMBER/MPI version on 8 nodes
--------------------------------------------------------------------------------
4. RESULTS
--------------------------------------------------------------------------------
| # of SOLUTE degrees of freedom (RNDFP): 3871.
| # of SOLVENT degrees of freedom (RNDFS): 0.
| NDFMIN = 3871. NUM_NOSHAKE = 0 CORRECTED RNDFP = 3871.
| TOTAL # of degrees of freedom (RNDF) = 3871.
---------------------------------------------------
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 = 821
| TOTAL SIZE OF NONBOND LIST = 6139
NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS = 0.0
Etot = 14868.0973 EKtot = 0.0000 EPtot = 14868.0973
BOND = 0.0035 ANGLE = 0.0236 DIHED = 0.0000
1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = -0.5310
EELEC = 15009.0019 EHBOND = 0.0000 RESTRAINT = 0.0000
EPOLZ = -140.4008
Dipole convergence: rms = 0.534E+00 temperature = 0.00
------------------------------------------------------------------------------
vlimit exceeded for step 0; vmax = 40.5272
vlimit exceeded for step 1; vmax = 21.9963
vlimit exceeded for step 2; vmax = 20.7611
vlimit exceeded for step 3; vmax = 21.5506
vlimit exceeded for step 4; vmax = 21.1900
vlimit exceeded for step 5; vmax = 20.2041
vlimit exceeded for step 8; vmax = 20.1706
vlimit exceeded for step 10; vmax = 41.8294
vlimit exceeded for step 11; vmax = 25.7258
vlimit exceeded for step 12; vmax = 20.6003
vlimit exceeded for step 14; vmax = 20.3928
vlimit exceeded for step 15; vmax = 20.1408
vlimit exceeded for step 16; vmax = 21.9159
vlimit exceeded for step 19; vmax = 477.1597
vlimit exceeded for step 20; vmax = 2252.4681
vlimit exceeded for step 21; vmax = 14786.3329
vlimit exceeded for step 22; vmax = **********
vlimit exceeded for step 23; vmax = **********
vlimit exceeded for step 24; vmax = **********
vlimit exceeded for step 25; vmax = **********
vlimit exceeded for step 26; vmax = **********
vlimit exceeded for step 27; vmax = **********
vlimit exceeded for step 28; vmax = **********
vlimit exceeded for step 29; vmax = **********
vlimit exceeded for step 30; vmax = **********
vlimit exceeded for step 31; vmax = **********
vlimit exceeded for step 32; vmax = **********
vlimit exceeded for step 33; vmax = **********
vlimit exceeded for step 34; vmax = **********
vlimit exceeded for step 35; vmax = **********
vlimit exceeded for step 36; vmax = **********
vlimit exceeded for step 37; vmax = **********
vlimit exceeded for step 38; vmax = **********
vlimit exceeded for step 39; vmax = **********
vlimit exceeded for step 40; vmax = **********
vlimit exceeded for step 41; vmax = **********
vlimit exceeded for step 42; vmax = **********
vlimit exceeded for step 43; vmax = **********
vlimit exceeded for step 44; vmax = **********
vlimit exceeded for step 45; vmax = **********
vlimit exceeded for step 46; vmax = **********
vlimit exceeded for step 47; vmax = **********
vlimit exceeded for step 48; vmax = **********
vlimit exceeded for step 49; vmax = **********
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Received on Sun Sep 13 2015 - 18:00:02 PDT
