Hi there,
I'm new to amber and I'm trying to learn how to deal with it....
Within this spirit, I'm trying to perform a MD of an isolated system at
room temperature, therefore I have chosen to use the variable NTB=0. All
of the others are common values, I think.
But it isn't working as shows the output:
-------------------------------------------------------
Amber 7 SANDER Scripps/UCSF 2002
-------------------------------------------------------
| Tue Jul 29 15:10:12 2003
[-O]verwriting output
File Assignments:
| MDIN:
md0.in
| MDOUT:
md0.out
|INPCRD:
alphacd.crd
| PARM:
alphacd.top
|RESTRT:
restrt
| REFC:
refc
| MDVEL:
md0.vel
| MDEN:
md0.en
| MDCRD:
md0.crd
|MDINFO:
mdinfo
|INPDIP:
inpdip
|RSTDIP:
rstdip
Here is the input file:
# IMIN -> tipo de
simulacao
# NTX, IREST -> nature and format of
input
# NTWX, NTWV, NTWE, NTWR, NTPR -> nature ando format of
output
# NTB -> Periodic
boundary
# NSTLIM, NSCM -> MD run
flags
# NTT, TEMP0, TAUTP -> Temperature
regulation
# NTC ->
Shake
alpha-ciclodextrina isolada a temperatura ambiente
(equilibracao)
&cntrl
IMIN=0, IREST=0,
NTX=1,
NTWX=50, NTWV=50,
NTWR=50,
NTWE=50,
NTPR=50,
NSTLIM=5000,
NTB=0,
NSCM=100,
NTC=1,
NTT=1, TEMP0=298.15,
TAUTP=1.0,
&end
--------------------------------------------------------------------------------
1. RESOURCE USE:
--------------------------------------------------------------------------------
|
Flags:
| NONPERIODIC ntb=0 and igb=0: Setting up nonperiodic simulation
| New format PARM file being parsed.
| Version = 1.000 Date = 06/17/03 Time = 17:07:40
NATOM = 126 NTYPES = 6 NBONH = 60 MBONA = 65
NTHETH = 134 MTHETA = 90 NPHIH = 287 MPHIA = 192
NHPARM = 0 NPARM = 0 NNB = 661 NRES = 1
NBONA = 65 NTHETA = 90 NPHIA = 192 NUMBND = 6
NUMANG = 11 NPTRA = 12 NATYP = 6 NPHB = 0
IFBOX = 0 NMXRS = 126 IFCAP = 0 NEXTRA = 0
| Memory Use Allocated Used
| Real 2000000 9471
| Hollerith 400000 759
| Integer 2000000 418848
| Max Nonbonded Pairs: 5400000
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals
--------------------------------------------------------------------------------
2. CONTROL DATA FOR THE RUN
--------------------------------------------------------------------------------
ACD
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 = 50, ntrx = 1, ntwr
= 50
iwrap = 0, ntwx = 50, ntwv = 50, ntwe
= 50
ioutfm = 0, ntwprt = 0, idecomp = 0,
rbornstat= 0
Potential function:
ntf = 1, ntb = 0, 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 = 0
Molecular dynamics:
nstlim = 5000, nscm = 100, nrespa = 1
t = 0.00000, dt = 0.00100, vlimit = 20.00000
Temperature regulation:
ig = 71277, ntt = 1, vrand = 0
temp0 = 298.15000, tempi = 0.00000, heat = 0.00000
dtemp = 5.00000, tautp = 1.00000
--------------------------------------------------------------------------------
3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------
ACD
begin time read from input coords = 0.000 ps
Number of triangulated 3-point waters found: 0
Sum of charges from parm topology file = 0.00200000
Forcing neutrality...
--------------------------------------------------------------------------------
4. RESULTS
--------------------------------------------------------------------------------
---------------------------------------------------
eedmeth=4: Setting switch to one everywhere
---------------------------------------------------
| Local SIZE OF NONBOND LIST = 5578
| TOTAL SIZE OF NONBOND LIST = 5578
NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS = 0.0
Etot = nan EKtot = 0.0000 EPtot = nan
BOND = 4.0519 ANGLE = nan DIHED = 73.9878
1-4 NB = 23.5207 1-4 EEL = 619.4757 VDWAALS = 59562.8837
EELEC = -389.5910 EHBOND = 0.0000 RESTRAINT = 0.0000
------------------------------------------------------------------------------
vlimit exceeded for step 0; vmax = 93.6575435
vlimit exceeded for step 1; vmax = 20.5330838
vlimit exceeded for step 2; vmax = 8790956.85
vlimit exceeded for step 3; vmax = 3218.44947
vlimit exceeded for step 4; vmax = 186.852475
vlimit exceeded for step 5; vmax = 281.72415
vlimit exceeded for step 6; vmax = 305.697176
vlimit exceeded for step 7; vmax = 302.390465
vlimit exceeded for step 8; vmax = 221.471003
vlimit exceeded for step 9; vmax = 178.076931
vlimit exceeded for step 10; vmax = 173.338029
vlimit exceeded for step 11; vmax = 434.991607
vlimit exceeded for step 12; vmax = 147.34334
vlimit exceeded for step 13; vmax = 80.8046939
vlimit exceeded for step 14; vmax = 80.5587922
vlimit exceeded for step 15; vmax = 1471.60039
vlimit exceeded for step 16; vmax = 80.0696426
vlimit exceeded for step 17; vmax = 79.8330323
vlimit exceeded for step 18; vmax = 79.6017966
vlimit exceeded for step 19; vmax = 79.3746615
vlimit exceeded for step 20; vmax = 79.1385957
vlimit exceeded for step 21; vmax = 78.8850897
vlimit exceeded for step 22; vmax = 78.5758855
vlimit exceeded for step 23; vmax = 78.2741297
vlimit exceeded for step 24; vmax = 77.9481826
vlimit exceeded for step 25; vmax = 85.172779
vlimit exceeded for step 26; vmax = 77.2745741
vlimit exceeded for step 27; vmax = 76.9446935
vlimit exceeded for step 28; vmax = 76.627078
vlimit exceeded for step 29; vmax = 3397.81899
vlimit exceeded for step 30; vmax = 76.0964907
vlimit exceeded for step 31; vmax = 75.9137909
vlimit exceeded for step 32; vmax = 75.8097905
vlimit exceeded for step 33; vmax = 75.7734782
vlimit exceeded for step 34; vmax = 75.7649366
vlimit exceeded for step 35; vmax = 75.7567528
vlimit exceeded for step 36; vmax = 75.7495732
vlimit exceeded for step 37; vmax = 75.7434868
vlimit exceeded for step 38; vmax = 73488.7837
vlimit exceeded for step 39; vmax = 75.7328433
vlimit exceeded for step 40; vmax = 75.7284959
vlimit exceeded for step 41; vmax = 75.7245491
vlimit exceeded for step 42; vmax = 775.454355
vlimit exceeded for step 43; vmax = 75.7162903
vlimit exceeded for step 44; vmax = 75.711727
vlimit exceeded for step 45; vmax = 75.7068749
vlimit exceeded for step 46; vmax = 75.7020602
vlimit exceeded for step 47; vmax = 75.6975821
vlimit exceeded for step 48; vmax = 75.6935556
vlimit exceeded for step 49; vmax = 75.6901533
NSTEP = 50 TIME(PS) = 0.050 TEMP(K) = nan PRESS = 0.0
Etot = nan EKtot = nan EPtot = nan
BOND = 193318.0575 ANGLE = nan DIHED = 116.9248
1-4 NB = 2425.1376 1-4 EEL = 420.0159 VDWAALS = 8453.2431
EELEC = -170.1844 EHBOND = 0.0000 RESTRAINT = 0.0000
------------------------------------------------------------------------------
vlimit exceeded for step 50; vmax = 83.3956481
vlimit exceeded for step 51; vmax = 75.6851903
vlimit exceeded for step 52; vmax = 75.6834912
vlimit exceeded for step 53; vmax = 75.6818567
vlimit exceeded for step 54; vmax = 160.110583
vlimit exceeded for step 55; vmax = 75.6798846
vlimit exceeded for step 56; vmax = 75.6798899
vlimit exceeded for step 57; vmax = 413.502874
vlimit exceeded for step 58; vmax = 282.051973
vlimit exceeded for step 59; vmax = 75.679949
vlimit exceeded for step 60; vmax = 75.6799745
vlimit exceeded for step 61; vmax = 75.6800103
vlimit exceeded for step 62; vmax = 76.451566
vlimit exceeded for step 63; vmax = 75.680118
vlimit exceeded for step 64; vmax = 75.6801905
vlimit exceeded for step 65; vmax = 75.6802722
vlimit exceeded for step 66; vmax = 99.9119017
vlimit exceeded for step 67; vmax = 107.599584
vlimit exceeded for step 68; vmax = 75.680529
vlimit exceeded for step 69; vmax = 75.6806056
vlimit exceeded for step 70; vmax = 75.6806739
vlimit exceeded for step 71; vmax = 75.6807332
vlimit exceeded for step 72; vmax = 75.6807842
vlimit exceeded for step 73; vmax = 2198.5185
vlimit exceeded for step 74; vmax = 75.680913
vlimit exceeded for step 75; vmax = 75.6810012
vlimit exceeded for step 76; vmax = 75.6811096
vlimit exceeded for step 77; vmax = 75.6812408
vlimit exceeded for step 78; vmax = 114.163678
vlimit exceeded for step 79; vmax = 75.6815795
vlimit exceeded for step 80; vmax = 75.6627231
Frac coord min, max: -0.00356895655 0.680901547
The system has extended beyond
the extent of the virtual box.
Restarting sander will recalculate
a new virtual box with 30 Angstroms
extra on each side, if there is a
restart file for this configuration.
EWALD BOMB in subroutine Routine: map_coords (ew_force.f)
Atom out of bounds. If a restart has been written,
restarting should resolve the error
I do what the program asks and use the "-c restrt" option in sander and
change "NTX=5" and "IREST=1" in md0.in file, and it keeps falling in the
same errors until the output turns to be:
-------------------------------------------------------
Amber 7 SANDER Scripps/UCSF 2002
-------------------------------------------------------
| Tue Jul 29 15:17:29 2003
[-O]verwriting output
File Assignments:
| MDIN:
md0.in
| MDOUT:
md0.out
|INPCRD:
restrt
| PARM:
alphacd.top
|RESTRT:
restrt
| REFC:
refc
| MDVEL:
md0.vel
| MDEN:
md0.en
| MDCRD:
md0.crd
|MDINFO:
mdinfo
|INPDIP:
inpdip
|RSTDIP:
rstdip
Here is the input file:
# IMIN -> tipo de
simulacao
# NTX, IREST -> nature and format of
input
# NTWX, NTWV, NTWE, NTWR, NTPR -> nature ando format of
output
# NTB -> Periodic
boundary
# NSTLIM, NSCM -> MD run
flags
# NTT, TEMP0, TAUTP -> Temperature
regulation
# NTC ->
Shake
alpha-ciclodextrina isolada a temperatura ambiente
(equilibracao)
&cntrl
IMIN=0, IREST=1,
NTX=5,
NTWX=50, NTWV=50,
NTWR=50,
NTWE=50,
NTPR=50,
NSTLIM=5000,
NTB=0,
NSCM=100,
NTC=1,
NTT=1, TEMP0=298.15,
TAUTP=1.0,
&end
--------------------------------------------------------------------------------
1. RESOURCE USE:
--------------------------------------------------------------------------------
|
Flags:
| NONPERIODIC ntb=0 and igb=0: Setting up nonperiodic simulation
| New format PARM file being parsed.
| Version = 1.000 Date = 06/17/03 Time = 17:07:40
NATOM = 126 NTYPES = 6 NBONH = 60 MBONA = 65
NTHETH = 134 MTHETA = 90 NPHIH = 287 MPHIA = 192
NHPARM = 0 NPARM = 0 NNB = 661 NRES = 1
NBONA = 65 NTHETA = 90 NPHIA = 192 NUMBND = 6
NUMANG = 11 NPTRA = 12 NATYP = 6 NPHB = 0
IFBOX = 0 NMXRS = 126 IFCAP = 0 NEXTRA = 0
Static Integer Memory requirement of: 2412704 exceeds MAXINT of
2000000
| Memory Use Allocated Used
| Real 2000000 10412
| Hollerith 400000 759
| Integer 2000000 2412704
| Max Nonbonded Pairs: 5400000
** Redimension and recompile
What is wrong?? I'd appreciate any help....
Thanks in advance,
Herbert
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Received on Tue Jul 29 2003 - 19:53:00 PDT
