[AMBER] What is wrong with the minimization?

From: Huggins, Esther, C <esther.huggins273.topper.wku.edu>
Date: Mon, 14 Sep 2015 00:30:50 +0000

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
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