AMBER Archive (2006)

Subject: AMBER: pmf input files

From: Lauren O'Neil (lhunter2_at_nd.edu)
Date: Wed Aug 16 2006 - 12:20:45 CDT

Hello all,
I have a question regarding pmf input files. I am new to pmf calcs and
I prepared my input files just as they look in the amber 8 manual just
to get started. I am looking at a torsional angle in a DNA duplex. My
input files are attached. When I run the simulation it just gets
"stuck" when reading the restraints. My output file is also attached.
I assume that the problem is in the formatting of my chi.RST file, but
I'm not sure where. Thanks in advance.

Lauren O'Neil
Wiest Group
U. of Notre Dame

test of PMF
 &cntrl
 scee=1.2,
 ntpr=50, ntwx=5000,
 tempi=300.0, temp0=300.0, ntt=3,
 nstlim=50000, dt=0.002, ntf=2,
 ntb=2, ntp=1, pres0=1.0,
 taup=2.0, cut=10, nmropt=1,
 ntr=1, gamma_ln=1.0,
 irest=1, ntx=7,
/
&wt type='DUMPFREQ', istep1=10 /
&wt type='END' /
DISANG=chi.RST
DUMPAVE=chi_vs_t.298
&end


          -------------------------------------------------------
          Amber 8 SANDER Scripps/UCSF 2004
          -------------------------------------------------------

| Run on 08/16/2006 at 13:27:05
  [-O]verwriting output

File Assignments:
| MDIN: pmf.in
| MDOUT: pmf298.out
|INPCRD: mdNPT.restrt
| PARM: seq1pmf.prmtop
|RESTRT: pmf298.restrt
| REFC: mdNPT.restrt
| MDVEL: mdvel
| MDEN: mden
| MDCRD: pmf298.cmd
|MDINFO: mdinfo
|INPDIP: inpdip
|RSTDIP: rstdip

 
 Here is the input file:
 
test of PMF
 &cntrl
         scee=1.2,
        ntpr=50, ntwx=5000,
         tempi=300.0, temp0=300.0, ntt=3,
         nstlim=50000, dt=0.002, ntf=2,
         ntb=2, ntp=1, pres0=1.0,
         taup=2.0, cut=10, nmropt=1,
         ntr=1, gamma_ln=1.0,
         irest=1, ntx=7,
 /
 &wt type='DUMPFREQ', istep1=10 /
 &wt type='END' /
DISANG=chi.RST
DUMPAVE=chi_vs_t.298
                                                                               

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

| Flags: MPI HAS_10_12
 getting new box info from bottom of inpcrd
| peek_ewald_inpcrd: Box info found
|Largest sphere to fit in unit cell has radius = 22.835
| New format PARM file being parsed.
| Version = 1.000 Date = 08/08/06 Time = 14:44:13
 NATOM = 15126 NTYPES = 18 NBONH = 14446 MBONA = 730
 NTHETH = 862 MTHETA = 1130 NPHIH = 1671 MPHIA = 2038
 NHPARM = 0 NPARM = 0 NNB = 24487 NRES = 4756
 NBONA = 730 NTHETA = 1130 NPHIA = 2038 NUMBND = 43
 NUMANG = 89 NPTRA = 49 NATYP = 29 NPHB = 1
 IFBOX = 1 NMXRS = 34 IFCAP = 0 NEXTRA = 0
 NCOPY = 0

| Memory Use Allocated
| Real 1181123
| Hollerith 95514
| Integer 886815
| Max Pairs 4356288
| Max Rstack 698810
| Max Istack 75630
| Total 35836 kbytes
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals

     BOX TYPE: RECTILINEAR

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

                                                                                

General flags:
     imin = 0, nmropt = 1

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

Nature and format of output:
     ntxo = 1, ntpr = 50, ntrx = 1, ntwr = 500
     iwrap = 0, ntwx = 5000, ntwv = 0, ntwe = 0
     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 = 10.00000, intdiel = 1.00000
     scnb = 2.00000, scee = 1.20000

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

Molecular dynamics:
     nstlim = 50000, nscm = 1000, nrespa = 1
     t = 0.00000, dt = 0.00200, vlimit = 20.00000

Langevin dynamics temperature regulation:
     ig = 71277
     temp0 = 300.00000, tempi = 300.00000, gamma_ln= 1.00000

Pressure regulation:
     ntp = 1
     pres0 = 1.00000, comp = 44.60000, taup = 2.00000

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

Ewald parameters:
     verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1
     vdwmeth = 1, eedmeth = 1, netfrc = 1
     Box X = 45.671 Box Y = 46.463 Box Z = 71.017
     Alpha = 90.000 Beta = 90.000 Gamma = 90.000
     NFFT1 = 48 NFFT2 = 48 NFFT3 = 72
     Cutoff= 10.000 Tol =0.100E-04
     Ewald Coefficient = 0.27511
     Interpolation order = 4

    LOADING THE CONSTRAINED ATOMS AS GROUPS

   5. REFERENCE ATOM COORDINATES

      


# torsion restraint for dimer flipping
  &rst iat=220,221,224,225, r1=120., r2=298., r3=298., r4=120., rk2=30., rk3=30., /

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