AMBER Archive (2004)

Subject: AMBER: SANDER - Abnormal high velocities

From: Miguel de Federico (miguel_at_qorws1.uab.es)
Date: Wed Jan 28 2004 - 05:16:45 CST

 I'm trying to run a MD in vacuum heating from 0K to 298K in 20ps. I used one
imput file I had used succesfully, but now there is someting wrong with atom
velocities and temperature control. From the very beginnig of the simulation,
the velocities of the atoms are too high, and I can't find the reason. The
starting structure was fully minimized previous to the MD run.

 Here is the output file (which includes input as well).

 Thank you for any help,

Miguel.

XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
          -------------------------------------------------------
          Amber 7 SANDER Scripps/UCSF 2002
          -------------------------------------------------------

| Thu Jan 22 12:23:54 2004

  [-O]verwriting output

File Assignments:
| MDIN: 005dm0-298vacio.in
| MDOUT: 011aro.out
|INPCRD: 010aro.rst
| PARM: ../5leap/010aro.top
|RESTRT: 011aro.rst
| REFC: refc
| MDVEL: mdvel
| MDEN: mden
| MDCRD: 011aro.trj
|MDINFO: 011aro.inf
|INPDIP: inpdip
|RSTDIP: rstdip

 Here is the input file:

Dinamica molecular
Calentamiento de 0 a 298k
Volumen constante
 &cntrl
  imin=0, ntx=1, irest=0,
  ntwe=0, ntpr=10000,
  ntf=2, ntb=0, scnb=2.0, scee=1.2,
  ntt=1, tautp=0.2
  ntc=2,
  nstlim=40000,
  nmropt=1,
 &end
 &wt type='TEMP0', istep1=0, istep2=20000, value1=0.0, value2=298.0, &end
 &wt type='TEMP0', istep1=20000, istep2=40000, value1=298.0, value2=298.0,
&end
 &wt type='END'
 &end

--------------------------------------------------------------------------------
   1. RESOURCE USE:
--------------------------------------------------------------------------------

| Flags: SGIFFT HAS_FTN_ERFC
| NONPERIODIC ntb=0 and igb=0: Setting up nonperiodic simulation
| New format PARM file being parsed.
| Version = 1.000 Date = 01/22/04 Time = 10:56:35
 NATOM = 118 NTYPES = 9 NBONH = 60 MBONA = 62
 NTHETH = 148 MTHETA = 78 NPHIH = 218 MPHIA = 124
 NHPARM = 0 NPARM = 0 NNB = 640 NRES = 10
 NBONA = 62 NTHETA = 78 NPHIA = 124 NUMBND = 14
 NUMANG = 27 NPTRA = 16 NATYP = 12 NPHB = 0
 IFBOX = 0 NMXRS = 19 IFCAP = 0 NEXTRA = 0

| Memory Use Allocated Used
| Real 4000000 9039
| Hollerith 800000 720
| Integer 4000000 461793

| Max Nonbonded Pairs:10800000
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals

--------------------------------------------------------------------------------
   2. CONTROL DATA FOR THE RUN
--------------------------------------------------------------------------------

BAX

General flags:
     imin = 0, nmropt = 1

Nature and format of input:
     ntx = 1, irest = 0, ntrx = 1

Nature and format of output:
     ntxo = 1, ntpr = 10000, ntrx = 1, ntwr =
500
     iwrap = 0, ntwx = 0, ntwv = 0, ntwe =
0
     ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat=
0

Potential function:
     ntf = 2, ntb = 0, igb = 0, nsnb =
25
     ipol = 0, gbsa = 0
     dielc = 1.00000, cut = 8.00000, intdiel = 1.00000
     scnb = 2.00000, scee = 1.20000

Frozen or restrained atoms:
     ibelly = 0, ntr = 0

Molecular dynamics:
     nstlim = 40000, nscm = 1000, nrespa = 1
     t = 0.00000, dt = 0.00100, vlimit = 20.00000

Temperature regulation:
     ig = 71277, ntt = 1, vrand = 0
     temp0 = 300.00000, tempi = 0.00000, heat = 0.00000
     dtemp = 5.00000, tautp = 0.20000

SHAKE:
     ntc = 2, jfastw = 0
     tol = 0.00001

NMR refinement options:
     iscale = 0, noeskp = 1, ipnlty = 1, mxcub =
1
     scalm = 100.00000, pencut = 0.10000, tausw = 0.10000

--------------------------------------------------------------------------------
   3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------

BAX
 begin time read from input coords = 0.000 ps

           Begin reading energy term weight changes/NMR restraints
 WEIGHT CHANGES:
 TEMP0 0 20000 0.000000 298.000000 0 0
 TEMP0 20000 40000 298.000000 298.000000 0 0

 RESTRAINTS:
                          ** No restraint defined **

                  Done reading weight changes/NMR restraints

 Number of triangulated 3-point waters found: 0

     Sum of charges from parm topology file = -0.00102000
     Forcing neutrality...

--------------------------------------------------------------------------------
   4. RESULTS
--------------------------------------------------------------------------------

 ---------------------------------------------------

     eedmeth=4: Setting switch to one everywhere

 ---------------------------------------------------
| Local SIZE OF NONBOND LIST = 2191
| TOTAL SIZE OF NONBOND LIST = 2191

 NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS = 0.0
 Etot = 106.1587 EKtot = 0.0000 EPtot = 106.1587
 BOND = 3.7272 ANGLE = 13.2282 DIHED = 22.9198
 1-4 NB = 24.3777 1-4 EEL = 233.3656 VDWAALS = -2.3045
 EELEC = -189.1553 EHBOND = 0.0000 RESTRAINT = 0.0000
 
------------------------------------------------------------------------------

===============================================================================
                      NMR restraints for step 0
 Energy (this step): Bond = 0.000 Angle = 0.000 Torsion = 0.000
 Energy (tot. run) : Bond = 0.000 Angle = 0.000 Torsion = 0.000

 DEVIATIONS: Target=(r2+r3)/2 Target = closer of r2/r3
            This step Entire run This step Entire run
           ave. rms ave. rms ave. rms ave. rms
 Bond 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
 Angle 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
 Torsion 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
===============================================================================
 vlimit exceeded for step 1; vmax = 46.48517502200085
 vlimit exceeded for step 3; vmax = 30.01274959148688
 vlimit exceeded for step 4; vmax = 21.63378837713158
 vlimit exceeded for step 119; vmax = 21.27854452114763
 vlimit exceeded for step 120; vmax = 20.06039998968019
 vlimit exceeded for step 237; vmax = 66.61470830139494
 vlimit exceeded for step 238; vmax = 20.25206453025764
 vlimit exceeded for step 239; vmax = 20.32998938781406
 vlimit exceeded for step 240; vmax = 26.67620980927182
 vlimit exceeded for step 241; vmax = 20.43760414434990
 vlimit exceeded for step 242; vmax = 25.38570570731615
 [...]
 vlimit exceeded for step 17517; vmax = 26.11162099487474
 vlimit exceeded for step 17524; vmax = 21.34427205020697
 vlimit exceeded for step 17545; vmax = 22.03267533772302
 Frac coord min, max: -4.0586335982794037E-06 0.6788302040824691
 The system has extended beyond
     the extent of the virtual box.
 Restarting sander will recalculate
    a new virtual box with 30 Angstroms
    extra on each side, if there is a
    restart file for this configuration.
 EWALD BOMB in subroutine Routine: map_coords (ew_force.f)
 Atom out of bounds. If a restart has been written,
 restarting should resolve the error

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