This are the first steps of the simulation. I killed this job, but I can
provide , if there is need, a longer output.
-------------------------------------------------------
Amber 8 SANDER Scripps/UCSF 2004
-------------------------------------------------------
| Run on 08/30/2004 at 10:18:44
[-O]verwriting output
File Assignments:
| MDIN: heat+eqln.inp
| MDOUT: mdout
|INPCRD: x_na1.rst
| PARM: x_na.prmtop
|RESTRT: x_na2_lent_ca.rst
| REFC: x_na1.rst
| MDVEL: mdvel
| MDEN: mden
| MDCRD: mdcrd
|MDINFO: mdinfo
|INPDIP: inpdip
|RSTDIP: rstdip
Here is the input file:
Molecular dynamics script
&cntrl
imin=0
nstlim=400000, ntt=3,gamma_ln=1,
ntpr=50, pencut=0.1, ntwx = 50,
ntwe =50,
cut=16,
vlimit=10,
ntb=0,
ntc=2, nmropt=1,
&end
constrain ca
10
search
CA * M *
find
end
end
&ewald
eedmeth=5
&end
&wt
type='TEMP0', istep1=0, istep2=35000, value1=0.0, value2=100.0, /
&wt
type='TEMP0', istep1=35001, istep2=70000, value1=100.0, value2=200.0, /
&wt
type='TEMP0', istep1=70001, istep2=100000, value1=200.0, value2=300.0,
/
&wt
type='TEMP0', istep1=100001, istep2=400000, value1=300.0, value2=300.0,
/
&wt
type='END' /
--------------------------------------------------------------------------------
1. RESOURCE USE:
--------------------------------------------------------------------------------
| Flags:
| NONPERIODIC ntb=0 and igb=0: Setting up nonperiodic simulation
|Largest sphere to fit in unit cell has radius = 66.526
| New format PARM file being parsed.
| Version = 1.000 Date = 08/24/04 Time = 11:43:08
NATOM = 6304 NTYPES = 15 NBONH = 3047 MBONA = 3330
NTHETH = 7062 MTHETA = 4535 NPHIH = 13354 MPHIA = 9745
NHPARM = 0 NPARM = 0 NNB = 35072 NRES = 430
NBONA = 3330 NTHETA = 4535 NPHIA = 9745 NUMBND = 43
NUMANG = 93 NPTRA = 49 NATYP = 30 NPHB = 0
IFBOX = 0 NMXRS = 24 IFCAP = 0 NEXTRA = 0
NCOPY = 0
| Memory Use Allocated
| Real 415754
| Hollerith 38256
| Integer 1455716
| Max Pairs 12254976
| Max Rstack 113040
| Max Istack 31520
| Total 57961 kbytes
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals
--------------------------------------------------------------------------------
2. CONTROL DATA FOR THE RUN
--------------------------------------------------------------------------------
General flags:
imin = 0, nmropt = 1
Nature and format of input:
ntx = 1, irest = 0, ntrx = 1
Nature and format of output:
ntxo = 1, ntpr = 50, ntrx = 1, ntwr =
500
iwrap = 0, ntwx = 50, ntwv = 0, ntwe =
50
ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat=
0
Potential function:
ntf = 1, ntb = 0, igb = 0, nsnb =
25
ipol = 0, gbsa = 0, iesp = 0
dielc = 1.00000, cut = 16.00000, intdiel = 1.00000
scnb = 2.00000, scee = 1.20000
Frozen or restrained atoms:
ibelly = 0, ntr = 0
Molecular dynamics:
nstlim = 400000, nscm = 1000, nrespa = 1
t = 0.00000, dt = 0.00100, vlimit = 10.00000
Langevin dynamics temperature regulation:
ig = 71277
temp0 = 300.00000, tempi = 0.00000, gamma_ln= 1.00000
SHAKE:
ntc = 2, jfastw = 0
tol = 0.00001
NMR refinement options:
iscale = 0, noeskp = 1, ipnlty = 1, mxsub =
1
scalm = 100.00000, pencut = 0.10000, tausw = 0.10000
--------------------------------------------------------------------------------
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 0 35000 0.000000 100.000000 0 0
TEMP0 35001 70000 100.000000 200.000000 0 0
TEMP0 70001 100000 200.000000 300.000000 0 0
TEMP0 100001 400000 300.000000 300.000000 0 0
RESTRAINTS:
** No restraint defined **
Done reading weight changes/NMR restraints
Number of triangulated 3-point waters found: 0
Sum of charges from parm topology file = -0.00000047
Forcing neutrality...
--------------------------------------------------------------------------------
4. RESULTS
--------------------------------------------------------------------------------
---------------------------------------------------
eedmeth=5: Using 1/r dielectric
---------------------------------------------------
| Local SIZE OF NONBOND LIST = 3224429
| TOTAL SIZE OF NONBOND LIST = 3224429
NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS =
0.0
Etot = -3810.6919 EKtot = 0.0000 EPtot =
-3810.6919
BOND = 218.8366 ANGLE = 951.6952 DIHED =
3936.4964
1-4 NB = 1276.1936 1-4 EEL = 6371.2105 VDWAALS =
-2448.1057
EELEC = -14117.0186 EHBOND = 0.0000 RESTRAINT =
0.0000
------------------------------------------------------------------------------
NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
===============================================================================
NSTEP = 50 TIME(PS) = 0.050 TEMP(K) = 15.22 PRESS =
0.0
Etot = -3304.0423 EKtot = 239.8629 EPtot =
-3543.9052
BOND = 206.7875 ANGLE = 1054.7072 DIHED =
3959.0853
1-4 NB = 1289.0443 1-4 EEL = 6367.8200 VDWAALS =
-2479.8637
EELEC = -13941.4858 EHBOND = 0.0000 RESTRAINT =
0.0000
------------------------------------------------------------------------------
NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
===============================================================================
NSTEP = 100 TIME(PS) = 0.100 TEMP(K) = 28.32 PRESS =
0.0
Etot = -2859.1804 EKtot = 446.3120 EPtot =
-3305.4924
BOND = 255.9120 ANGLE = 1172.4957 DIHED =
3979.4847
1-4 NB = 1289.9858 1-4 EEL = 6363.3274 VDWAALS =
-2481.6255
EELEC = -13885.0725 EHBOND = 0.0000 RESTRAINT =
0.0000
------------------------------------------------------------------------------
NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
===============================================================================
NSTEP = 150 TIME(PS) = 0.150 TEMP(K) = 41.17 PRESS =
0.0
Etot = -2465.8044 EKtot = 648.7614 EPtot =
-3114.5659
BOND = 302.9045 ANGLE = 1277.1544 DIHED =
4016.1194
1-4 NB = 1293.2318 1-4 EEL = 6365.1019 VDWAALS =
-2467.1688
EELEC = -13901.9090 EHBOND = 0.0000 RESTRAINT =
0.0000
------------------------------------------------------------------------------
NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
===============================================================================
NSTEP = 200 TIME(PS) = 0.200 TEMP(K) = 53.06 PRESS =
0.0
Etot = -2085.7407 EKtot = 836.0203 EPtot =
-2921.7610
BOND = 353.6672 ANGLE = 1361.9579 DIHED =
4046.4720
1-4 NB = 1293.5304 1-4 EEL = 6369.6712 VDWAALS =
-2434.4922
EELEC = -13912.5674 EHBOND = 0.0000 RESTRAINT =
0.0000
------------------------------------------------------------------------------
NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
===============================================================================
NSTEP = 250 TIME(PS) = 0.250 TEMP(K) = 66.68 PRESS =
0.0
Etot = -1695.4135 EKtot = 1050.6658 EPtot =
-2746.0793
BOND = 380.6981 ANGLE = 1452.2613 DIHED =
4059.9768
1-4 NB = 1312.0277 1-4 EEL = 6366.0306 VDWAALS =
-2461.5100
EELEC = -13855.5637 EHBOND = 0.0000 RESTRAINT =
0.0000
------------------------------------------------------------------------------
NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
===============================================================================
NSTEP = 300 TIME(PS) = 0.300 TEMP(K) = 78.52 PRESS =
0.0
Etot = -1300.9163 EKtot = 1237.3369 EPtot =
-2538.2532
BOND = 434.9664 ANGLE = 1567.9427 DIHED =
4093.2816
1-4 NB = 1306.9961 1-4 EEL = 6360.8800 VDWAALS =
-2460.6108
EELEC = -13841.7092 EHBOND = 0.0000 RESTRAINT =
0.0000
------------------------------------------------------------------------------
NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
===============================================================================
NSTEP = 350 TIME(PS) = 0.350 TEMP(K) = 89.48 PRESS =
0.0
Etot = -919.6005 EKtot = 1410.0507 EPtot =
-2329.6513
BOND = 474.8886 ANGLE = 1643.6900 DIHED =
4120.2951
1-4 NB = 1319.6168 1-4 EEL = 6367.5290 VDWAALS =
-2449.8313
EELEC = -13805.8394 EHBOND = 0.0000 RESTRAINT =
0.0000
------------------------------------------------------------------------------
NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
===============================================================================
NSTEP = 400 TIME(PS) = 0.400 TEMP(K) = 100.42 PRESS =
0.0
Etot = -596.9411 EKtot = 1582.3260 EPtot =
-2179.2671
BOND = 493.7875 ANGLE = 1722.6750 DIHED =
4124.0786
1-4 NB = 1325.3619 1-4 EEL = 6382.6767 VDWAALS =
-2434.9758
EELEC = -13792.8710 EHBOND = 0.0000 RESTRAINT =
0.0000
------------------------------------------------------------------------------
NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
===============================================================================
-------------------------------------------------------
Madalin G. Giambasu
Junior Research Assistant
Institute of Biochemistry of Romanian Academy of Science
Splaiul Independentei 296, 060031, Bucharest 17, Romania
Phone: (+4)021.223.90.69; FAX: (+4)021.223.90.68
-------------------------------------------------------
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Received on Thu Sep 02 2004 - 01:15:12 PDT
