AMBER Archive (2009)

Subject: [AMBER] ntwr

From: taufik.alsarraj_at_utoronto.ca
Date: Wed Apr 08 2009 - 16:45:01 CDT

Hi,
I am trying to write a .rst file during a minimization using this *.in file

System minimization -only Si atoms at the surface are fixed

  &cntrl
   imin = 1,
   maxcyc = 10000,
   ncyc = 5000,
   ntb = 1,
   ntr = 1,
   ntwr = -200,
   restraint_wt=10.0,
   restraintmask=':1@%Si',
   cut = 10
  /

this should theoretically write a new rst file every 200 steps. but it
does not. only one rst file is written at the end of the minimization.
Am i missing something?
i use
>
mpirun -np 8 -hostfile ../hostfile_node1 sander.MPI -O -i min2.in -o
\ system5.out -p system3.prmtop -c system4.rst \
-r system5.rst -ref system4.rst

The minimization runs fine, the *.out looks good

File Assignments:
| MDIN: min2.in
| MDOUT: system5.out
|INPCRD: system4.rst
| PARM: system3.prmtop
|RESTRT: system5.rst
| REFC: system4.rst
| MDVEL: mdvel
| MDEN: mden
| MDCRD: mdcrd
|MDINFO: mdinfo
|INPDIP: inpdip
|RSTDIP: rstdip

|INPTRA: inptraj
|

  Here is the input file:

System minimization -only Si atoms at the surface are fixed

  &cntrl
   imin = 1,
   maxcyc = 10000,
   ncyc = 5000,
   ntb = 1,
   ntr = 1,
   ntwr = -200,
   restraint_wt=10.0,
   restraintmask=':1@%Si',
   cut = 10
  /

--------------------------------------------------------------------------------
    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 = 35.252
| New format PARM file being parsed.
| Version = 1.000 Date = 04/07/09 Time = 10:07:39
  NATOM = 68429 NTYPES = 20 NBONH = 65885 MBONA = 2817
  NTHETH = 3786 MTHETA = 4633 NPHIH = 5521 MPHIA = 7887
  NHPARM = 0 NPARM = 0 NNB = 109031 NRES = 21452
  NBONA = 2817 NTHETA = 4633 NPHIA = 7887 NUMBND = 53
  NUMANG = 111 NPTRA = 51 NATYP = 37 NPHB = 1
  IFBOX = 1 NMXRS = 3520 IFCAP = 0 NEXTRA = 0
  NCOPY = 0

| Memory Use Allocated
| Real 4670468
| Hollerith 432028
| Integer 1789600
| Max Pairs 4926888
| nblistReal 821148
| nblist Int 2361920
| Total 80053 kbytes
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals

      BOX TYPE: RECTILINEAR

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

MOL

General flags:
      imin = 1, 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
= -200
      iwrap = 0, ntwx = 0, ntwv = 0, ntwe
= 0
      ioutfm = 0, ntwprt = 0, idecomp = 0,
rbornstat= 0

Potential function:
      ntf = 1, ntb = 1, igb = 0, nsnb
= 25
      ipol = 0, gbsa = 0, iesp = 0
      dielc = 1.00000, cut = 10.00000, intdiel = 1.00000
      scnb = 2.00000, scee = 1.20000

Frozen or restrained atoms:
      ibelly = 0, ntr = 1

Energy minimization:
      maxcyc = 10000, ncyc = 5000, ntmin = 1
      dx0 = 0.01000, drms = 0.00010

Ewald parameters:
      verbose = 0, ew_type = 0, nbflag = 1, use_pme
= 1
      vdwmeth = 1, eedmeth = 1, netfrc = 0
      Box X = 70.504 Box Y = 97.755 Box Z = 119.727
      Alpha = 90.000 Beta = 90.000 Gamma = 90.000
      NFFT1 = 72 NFFT2 = 100 NFFT3 = 120
      Cutoff= 10.000 Tol =0.100E-04
      Ewald Coefficient = 0.27511
      Interpolation order = 4

| MPI Timing options:
| profile_mpi = 0

     LOADING THE CONSTRAINED ATOMS AS GROUPS

    5. REFERENCE ATOM COORDINATES

   MOL
      Mask :1@%Si; matches 320 atoms

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