AMBER Archive (2005)

Subject: AMBER: Restrained-MD

From: Ananda Rama Krishnan Selvaraj (ananda.selvaraj_at_chemie.uni-halle.de)
Date: Mon Jun 13 2005 - 18:04:14 CDT

Dear Amber Users,
                    i am doing MD simulation for organic molecules (each
molecule contains 102 atoms) with restraints..i am getting the following
error. could anyone inform the reason for this error.,

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

| Tue Jun 14 00:54:53 2005

  [-O]verwriting output

File Assignments:
| MDIN: dyn.in
       
| MDOUT: sander.out
       
|INPCRD: inpcrd
       
| PARM: prmtop
       
|RESTRT: dyn.rst
       
| REFC: refc
       
| MDVEL: mdvel
       
| MDEN: mden
       
| MDCRD: mdcrd
       
|MDINFO: mdinfo
       
|INPDIP: inpdip
       
|RSTDIP: rstdip
       

 
 Here is the input file:
 
MD_simulation of 64_PIMB in PBC_1
       
 &cntrl
       
   imin = 0, irest = 0, ntx = 1,
       
   ntt = 1, temp0 = 300.0, tautp = 1, gamma_ln = 10,
       
   ntp = 0,
       
   ntb = 1, ntc = 2, ntf = 2,
       
   nstlim = 10000,
       
   tempi = 0.0, dt = .0005,
       
   cut = 8.0, scee = 1.2,
       
   ntr = 1, ntpr = 100, ntwx = 100,
       
 &end
       
keep PIB fixed with weak constraints
       
10.0
       
RES 1 65
       
END
       
END
       

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

| Flags: ISTAR2 MPI
        
 getting new box info from bottom of inpcrd
| peek_ewald_inpcrd: Box info found
| INFO: Old style PARM file read

 NATOM = 6528 NTYPES = 10 NBONH = 0 MBONA = 6784
 NTHETH = 0 MTHETA = 11520 NPHIH = 0 MPHIA = 16128
 NHPARM = 0 NPARM = 0 NNB = 33664 NRES = 64
 NBONA = 6784 NTHETA = 11520 NPHIA = 16128 NUMBND = 37
 NUMANG = 136 NPTRA = 70 NATYP = 10 NPHB = 0
 IFBOX = 1 NMXRS = 102 IFCAP = 0 NEXTRA = 0

| Memory Use Allocated Used
| Real 2000000 553165
| Hollerith 400000 39234
| Integer 2000000 1028007

| Max Nonbonded Pairs: 5400000
| Duplicated 0 dihedrals
| Duplicated 768 dihedrals

     BOX TYPE: RECTILINEAR

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

     PIB
        

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 = 100, ntrx = 1, ntwr =
    500
     iwrap = 0, ntwx = 100, ntwv = 0, ntwe =
      0
     ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat=
     0

Potential function:
     ntf = 2, ntb = 1, 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 = 1

Molecular dynamics:
     nstlim = 10000, nscm = 1000, nrespa = 1
     t = 0.00000, dt = 0.00050, vlimit = 20.00000

Temperature regulation:
     ig = 71277, ntt = 1, vrand = 0
     temp0 = 300.00000, tempi = 0.00000, heat = 0.00000
     dtemp = 5.00000, tautp = 1.00000

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

Ewald parameters:
     verbose = 0, ew_type = 0, nbflag = 1, use_pme =
      1
     vdwmeth = 1, eedmeth = 1, frc_int = 0, netfrc =
      1
     Box X = 180.000 Box Y = 40.000 Box Z = 20.000
     Alpha = 90.000 Beta = 90.000 Gamma = 90.000
     NFFT1 = 180 NFFT2 = 40 NFFT3 = 20
     Cutoff= 8.000 Tol =0.100E-04
     Ewald Coefficient = 0.34864
     Interpolation order = 4
| PLEVEL = 1: runmd parallelization, no EKCMR

  Unit 10 Error on OPEN: refc
                                   

thanks..anand

ANANDA RAMA KRISHNAN .S
PhD Student
c/o. Prof. Rudolf Friedemann
Department of organic chemistry
Martin Luther university
Kurt-mothes-str.2
D-06120 Halle (saale),Germany
e-mail: ananda.selvaraj_at_chemie.uni-halle.de
Ph(lab) : (+int) 345 - 5525683
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