AMBER Archive (2008)

Subject: AMBER: output file AMBER9_MPI

From: Vijay Manickam Achari (vjrajamany_at_yahoo.com)
Date: Thu Jun 26 2008 - 14:06:19 CDT

Dear Amber experts,

I am running MD production run in cluster.

After I submit the job, the simulaiton 'HANG' and there is no any further out put.

Here I copy the output data where it hangs..

****************************************************************************

          -------------------------------------------------------
          Amber 9 SANDER 2006
          -------------------------------------------------------

| Run on 06/27/2008 at 02:54:45
  [-O]verwriting output

File Assignments:
| MDIN: MD-betaMalto-LyoLowS1.in
| MDOUT: betaMalto-lyolowS1-MD01-run0000.out
|INPCRD: malto-lyolowEqui2-equi21.rst_10000
| PARM: mal-lyoLOW-shif.top
|RESTRT: betaMalto-lyolowS1-MD01-run0100.rst
| REFC: refc
| MDVEL: mdvel
| MDEN: mden
| MDCRD: betaMalto-lyolowS1-MD01-run0000.traj
|MDINFO: mdinfo
|INPDIP: inpdip
|RSTDIP: rstdip

 
 Here is the input file:
 
Dynamic Simulation with Constant Pressure
 &cntrl
   imin=0,
   irest=1, ntx=7,
   ntxo=1,
   scnb=1.0, scee=1.0,
   ntt=3, tempi = 300.0, temp0=300.0, tautp=0.2,
   ntb = 2, ntp=1, taup=0.2,
   ntf=2,ntc=2,
   nstlim=100000, dt=0.001,
   ntwe=100, ntwx=100, ntpr=100, ntwr=-50000,
   ntr=0
 /
                                                                               

--------------------------------------------------------------------------------
   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 = 23.888
| New format PARM file being parsed.
| Version = 1.000 Date = 06/23/08 Time = 17:06:22
 NATOM = 23736 NTYPES = 9 NBONH = 14776 MBONA = 9216
 NTHETH = 27648 MTHETA = 12032 NPHIH = 45312 MPHIA = 21248
 NHPARM = 0 NPARM = 0 NNB = 123552 NRES = 1256
 NBONA = 9216 NTHETA = 12032 NPHIA = 21248 NUMBND = 9
 NUMANG = 14 NPTRA = 20 NATYP = 9 NPHB = 1
 IFBOX = 1 NMXRS = 81 IFCAP = 0 NEXTRA = 0
 NCOPY = 0

| Memory Use Allocated
| Real 1296588
| Hollerith 143674
| Integer 1964637
| Max Pairs 164833
| nblistReal 284832
| nblist Int 1180797
| Total 25846 kbytes
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals

     BOX TYPE: RECTILINEAR

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

                                                                                

General flags:
     imin = 0, nmropt = 0

Nature and format of input:
     ntx = 7, irest = 1, ntrx = 1

Nature and format of output:
     ntxo = 1, ntpr = 100, ntrx = 1, ntwr = -50000
     iwrap = 0, ntwx = 100, ntwv = 0, ntwe = 100
     ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0

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

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

Molecular dynamics:
     nstlim = 100000, nscm = 1000, nrespa = 1
     t = 0.00000, dt = 0.00100, vlimit = 20.00000

Langevin dynamics temperature regulation:
     ig = 71277
     temp0 = 300.00000, tempi = 300.00000, gamma_ln= 0.00000

Pressure regulation:
     ntp = 1
     pres0 = 1.00000, comp = 44.60000, taup = 0.20000

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

Ewald parameters:
     verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1
     vdwmeth = 1, eedmeth = 1, netfrc = 1
     Box X = 91.975 Box Y = 47.775 Box Z = 50.453
     Alpha = 90.000 Beta = 90.000 Gamma = 90.000
     NFFT1 = 96 NFFT2 = 48 NFFT3 = 50
     Cutoff= 8.000 Tol =0.100E-04
     Ewald Coefficient = 0.34864
     Interpolation order = 4

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

                                                                                
 begin time read from input coords = 400.000 ps

 Number of triangulated 3-point waters found: 1000
| Atom division among processors:
| 0 405 810 1215 1620 2025 2430 2835
| 3240 3645 4050 4455 4860 5265 5670 6075
| 6480 6885 7290 7695 8100 8505 8910 9315
| 9720 10125 10530 10935 11340 11745 12150 12555
| 12960 13365 13770 14175 14580 14985 15309 15633
| 15957 16281 16605 16929 17253 17577 17901 18225
| 18549 18873 19197 19521 19845 20169 20493 20817
| 21141 21465 21789 22113 22437 22761 23088 23412
| 23736

     Sum of charges from parm topology file = 0.00000000
     Forcing neutrality...
| Running AMBER/MPI version on 64 nodes

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

 ---------------------------------------------------
 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 = 0.3338E-14 at 2.509280
| CHECK d/dx switch(x): max rel err = 0.8261E-11 at 2.768360
 ---------------------------------------------------
| Local SIZE OF NONBOND LIST = 86720
| TOTAL SIZE OF NONBOND LIST = 5208818

*****************************************************************************

can anyone highligh what is the mistake in the simulation?

Thank you..

Vijay

Vijay Manickam Achari
(Phd Student c/o Prof Rauzah Hashim)
Chemistry Department,
University of Malaya,
Malaysia
vjramana_at_gmail.com

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