AMBER Archive (2004)Subject: AMBER: simulated annealing..
From: Abd Ghani Bin Abd Aziz (GS13161_at_mutiara.upm.edu.my)
Date: Wed Jul 28 2004  08:45:55 CDT
Dear Amber,
sorry..i forgot to type my problem... i already create a new script with
nmropt=1. i also removed the group definition (as your adviceactually i
want to restraint but at mean time i just want to see wether the
temperature can cool down or not). the script that i create, i put it at
the bottom of the email. as u mention about the output file, it seems that
everything is fine... but actually the problem still occured..the
temperature heat up untill 200++K and there at the end of simulation, the
temperature is still maintain (not recool to 10K)..
i paste also the output file for you to look at it..
thank you.
Abd Ghani
# Control section
&cntrl
ntwx = 250, ntpr = 50,
ntt = 1, temp0 = 400.0, tempi = 10.0, tautp = 1.0,
scnb = 2.0, scee = 1.2, dielc = 1, cut = 8.0,
ntb = 2, ntc = 2, ntf = 2,
nstlim = 21000, dt = 0.0010,
ntp = 1, taup = 0.1, comp = 44.6, pres0 = 1.0,
ibelly = 0, ntr = 0,
imin = 0, irest = 0, ntx = 1, nmropt = 1,
&end
&ewald
skinnb = 2.0,
nbflag = 1,
&end
&wt
type = 'TEMP0', istep1 = 1, istep2 = 2000, value1 = 10.0, value2 = 400.0,
&end
&wt
type = 'TEMP0', istep1 = 2001, istep2 = 3000, value1 = 400.0, value2 =
400.0,
&end
&wt
type = 'TEMP0', istep1 = 3001, istep2 = 21000, value1 = 400.0, value2 =
10.0,
&end
&wt
type='END'
&end
&rst
iat = 0,
&end
END
________________________________________________________________________
Here is the input file:
# Control section
&cntrl
ntwx = 250, ntpr = 50,
ntt = 1, temp0 = 400.0, tempi = 10.0, tautp = 1.0,
scnb = 2.0, scee = 1.2, dielc = 1, cut = 8.0,
ntb = 2, ntc = 2, ntf = 2,
nstlim = 21000, dt = 0.0010,
ntp = 1, taup = 0.1, comp = 44.6, pres0 = 1.0,
ibelly = 0, ntr = 0,
imin = 0, irest = 0, ntx = 1, nmropt = 1,
&end
&ewald
skinnb = 2.0,
nbflag = 1,
&end
&wt
type = 'TEMP0', istep1 = 1, istep2 = 2000, value1 = 10.0, value2 = 400.0,
&end
&wt
type = 'TEMP0', istep1 = 2001, istep2 = 3000, value1 = 400.0, value2 =
400.0,
&end
&wt
type = 'TEMP0', istep1 = 3001, istep2 = 21000, value1 = 400.0, value2 =
10.0,
&end
&wt
type='END'
&end
&rst
iat = 0,
&end
END

1. RESOURCE USE:
getting box info from bottom of parm
getting new box info from bottom of inpcrd
 peek_ewald_inpcrd: Box info found
EWALD SPECIFIC INPUT:
Largest sphere to fit in unit cell has radius = 32.575
Calculating ew_coeff from dsum_tol,cutoff
Box X = 79.791 Box Y = 79.791 Box Z = 79.791
Alpha = 109.471 Beta = 109.471 Gamma = 109.471
NFFT1 = 80 NFFT2 = 80 NFFT3 = 80
Cutoff= 8.000 Tol =0.100E04
Ewald Coefficient = 0.34864
Interpolation order = 4
NATOM = 33896 NTYPES = 17 NBONH = 31021 MBONA = 2952
NTHETH = 6594 MTHETA = 4023 NPHIH = 11772 MPHIA = 7184
NHPARM = 0 NPARM = 0 NNB = 69551 NRES = 9744
NBONA = 2952 NTHETA = 4023 NPHIA = 7184 NUMBND = 44
NUMANG = 94 NPTRA = 33 NATYP = 30 NPHB = 1
IFBOX = 2 NMXRS = 24 IFCAP = 0
EWALD MEMORY USE:
 Total heap storage needed = 1245
 Adjacent nonbond minimum mask = 69551
 Max number of pointers = 25
 List build maxmask = 139102
 Maximage = 49591
EWALD LOCMEM POINTER OFFSETS
 Real memory needed by PME = 1245
 Size of EEDTABLE = 20918
 Real memory needed by EEDTABLE = 83672
 Integer memory needed by ADJ = 139102
 Integer memory used by local nonb= 1232919
 Real memory used by local nonb = 555525
 MAX NONBOND PAIRS = 100000000
 Memory Use Allocated Used
 Real 10000000 1963082
 Hollerith 10000000 213122
 Integer 10000000 2119605
 Max Nonbonded Pairs:********
BOX TYPE: TRUNCATED OCTAHEDRON
2. CONTROL DATA FOR THE RUN
TIMLIM= 999999. IREST = 0 IBELLY= 0
IMIN = 0
IPOL = 0
NTX = 1 NTXO = 1
IG = 71277 TEMPI = 10.00 HEAT = 0.000
NTB = 2 BOXX = 79.791
BOXY = 79.791 BOXZ = 79.791
NTT = 1 TEMP0 = 400.000
DTEMP = 0.000 TAUTP = 1.000
VLIMIT= 0.000
NTP = 1 PRES0 = 1.000 COMP = 44.600
TAUP = 0.100 NPSCAL= 0
NTCM = 0 NSCM = 9999999
NSTLIM=21000 NTU = 1
T = 0.000 DT = 0.00100
NTC = 2 TOL = 0.00001 JFASTW = 0
NTF = 2 NSNB = 25
CUT = 8.000 SCNB = 2.000
SCEE = 1.200 DIELC = 1.000
NTPR = 50 NTWR = 50 NTWX = 250
NTWV = 0 NTWE = 0 IOUTFM= 0
NTWPRT= 0 NTWPR0= 0 NTAVE= 0
NTR = 0 NTRX = 1
TAUR = 0.00000 NMROPT= 1 PENCUT= 0.10000
IVCAP = 0 MATCAP= 0 FCAP = 1.500
OTHER DATA:
IFCAP = 0 NATCAP= 0 CUTCAP= 0.000
XCAP = 0.000 YCAP = 0.000 ZCAP = 0.000
VRAND= 0
NATOM = 33896 NRES = 9744
Water definition for fast triangulated model:
Resname = WAT ; Oxygen_name = O ; Hyd1_name = H1 ; Hyd2_name = H2
3. ATOMIC COORDINATES AND VELOCITIES
begin time read from input coords = 0.000 ps
Begin reading energy term weight changes/NMR restraints
WEIGHT CHANGES:
TEMP0 1 2000 10.000000 400.000000 0 0
TEMP0 2001 3000 400.000000 400.000000 0 0
TEMP0 3001 21000 400.000000 10.000000 0 0
RESTRAINTS:
No valid redirection requests found
** No restraint defined **
Done reading weight changes/NMR restraints
Number of triangulated 3point waters found: 9377
Sum of charges from parm topology file = 0.00000023
Forcing neutrality...

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 = 0.3242E14 at 2.436720
 CHECK d/dx switch(x): max rel err = 0.8156E11 at 2.782960

Total number of mask terms = 59876
Total number of mask terms = 119752
 Total Ewald setup time = 0.09999990


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