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.chemie.uni-halle.de
Ph(lab) : (+int) 345 - 5525683
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Received on Tue Jun 14 2005 - 00:53:00 PDT
