I have received your explanation and advice for my puzzles ,as following:
You should move carefully step by step. It looks like you are trying to
equilibrate the system and run targetted MD at the same time. Try the
following:
1. Make sure you can run ordinary dynamics. Turn off targeted dynamics,
set ntpr=1 and nstlim=50. Get your system equilibrated to 300K. (If you
have
problems at this stage, then you have a much simpler debugging strategy.)
2. You input file sets ntr=1, with a very large restraint weight. For that
part of the protein, nothing will be able to move. This will probably need
to
be changed.
3. Try very simple targeted MD runs once you have an equilibrated protein.
To get started, still set ntpr=1 and nstlim to some smallish value (say
100).
Use the simplest restraints you can think of and study the output carefully
to
try to understand exactly what is going on.
4. Your output says "old style PARM file read". This is somewhat
I have tried to solve my problems as you suggested. Firstly, I minimize
my system and my input file is :
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
initial minimisation of the protein
&cntrl
imin=1,
maxcyc=50000,
ncyc=25000,
cut=12.0,
ntb=0,
ntpr=20,
ntr=1,
restraintmask=':29-342.CA,N,C',
restraint_wt=200,
/
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Secondly, I heat my system through six steps separately with a very short
time and my input file is :
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Stage 1 heating of T 0 to 50K
&cntrl
imin=0, irest=0, ntx=1,
nstlim=50, dt=0.0005,
ntc=2, ntf=2,
ntt=1, tautp=1.0,
tempi=0.0, temp0=50.0,
ntpr=1, ntwx=1,
ntb=0, igb=1,
ntr=1,
restraintmask=':29-342.CA,N,C',
restraint_wt=200,
cut=999.,rgbmax=999.
/
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Stage 1 heating of T 50K to 100K
&cntrl
imin=0, irest=1, ntx=5,
nstlim=50, dt=0.0005,
ntc=2, ntf=2,
ntt=1, tautp=1.0,
tempi=50.0, temp0=100.0,
ntpr=1, ntwx=1,
ntb=0, igb=1,ntr=1,
restraintmask=':29-342.CA,N,C',
restraint_wt=200,
cut=999.0,rgbmax=999.
/
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
I heat tje system to 300K through the following four steps :100K-150K,
150K-200K,200K-250K ,250K-300K,
After doing that ,I run equilibration and my input file is as following:
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Stage 2 equilibration
&cntrl
imin=0, irest=1, ntx=5,
nstlim=10, dt=0.001,
ntc=2, ntf=2,
ntt=1, tautp=0.5,
tempi=300.0, temp0=300.0,
ntpr=1, ntwx=1,
ntb=0,igb=1,ntr=1,
restraintmask=':29-342.CA,N,C',
restraint_wt=10,
cut=999.,rgbmax=999.
/
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
The corresponding output file is :
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Amber 9 SANDER 2006
-------------------------------------------------------
| Run on 01/05/2002 at 21:52:14
[-O]verwriting output
File Assignments:
| MDIN: equil.in
| MDOUT:
equil.out
|INPCRD:
heat6.rst
| PARM:
2RH1.prmtop
|RESTRT:
equil.rst
| REFC:
heat6.rst
| MDVEL:
mdvel
| MDEN:
mden
| MDCRD:
equil.mdcrd
|MDINFO:
mdinfo
|INPDIP:
inpdip
|RSTDIP:
rstdip
|INPTRA:
inptraj
|
Here is the input file:
Stage 2 equilibration 1
0-5ns
&cntrl
imin=0, irest=1,
ntx=5,
nstlim=10,
dt=0.001,
ntc=2,
ntf=2,
ntt=1,
tautp=0.5,
tempi=300.0,
temp0=300.0,
ntpr=1,
ntwx=1,
ntb=0,igb=1,ntr=1,
restraintmask=':29-342.CA,N,C',
restraint_wt=10,
cut=999.,rgbmax=999.
/
--------------------------------------------------------------------------------
1. RESOURCE USE:
--------------------------------------------------------------------------------
|
Flags:
| New format PARM file being parsed.
| Version = 1.000 Date = 02/04/02 Time = 11:15:57
NATOM = 4475 NTYPES = 14 NBONH = 2257 MBONA = 2282
NTHETH = 5102 MTHETA = 3115 NPHIH = 9620 MPHIA = 7736
NHPARM = 0 NPARM = 0 NNB = 24804 NRES = 276
NBONA = 2282 NTHETA = 3115 NPHIA = 7736 NUMBND = 42
NUMANG = 89 NPTRA = 44 NATYP = 27 NPHB = 0
IFBOX = 0 NMXRS = 24 IFCAP = 0 NEXTRA = 0
NCOPY = 0
Implicit solvent radii are modified Bondi radii
(mbondi)
| Memory Use Allocated
| Real 251103
| Hollerith 27128
| Integer 252978
| Max Pairs 1
| nblistReal 0
| nblist Int 0
| Total 3055 kbytes
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals
--------------------------------------------------------------------------------
2. CONTROL DATA FOR THE RUN
--------------------------------------------------------------------------------
General flags:
imin = 0, nmropt = 0
Nature and format of input:
ntx = 5, irest = 1, ntrx = 1
Nature and format of output:
ntxo = 1, ntpr = 1, ntrx = 1, ntwr =
500
iwrap = 0, ntwx = 1, ntwv = 0, ntwe
= 0
ioutfm = 0, ntwprt = 0, idecomp = 0,
rbornstat= 0
Potential function:
ntf = 2, ntb = 0, igb = 1, nsnb
= 25
ipol = 0, gbsa = 0, iesp = 0
dielc = 1.00000, cut = 999.00000, intdiel = 1.00000
saltcon = 0.00000, offset = 0.09000, gbalpha= 1.00000
gbbeta = 0.00000, gbgamma = 0.00000, surften = 0.00500
rdt = 0.00000, rgbmax = 999.00000
alpb = 0
scnb = 2.00000, scee = 1.20000
Frozen or restrained atoms:
ibelly = 0, ntr = 1
Molecular dynamics:
nstlim = 10, nscm = 1000, nrespa = 1
t = 0.00000, dt = 0.00100, vlimit = 20.00000
Berendsen (weak-coupling) temperature regulation:
temp0 = 300.00000, tempi = 300.00000, tautp = 0.50000
SHAKE:
ntc = 2, jfastw = 0
tol = 0.00001
LOADING THE CONSTRAINED ATOMS AS GROUPS
5. REFERENCE ATOM COORDINATES
| INFO: Old style inpcrd file read
Mask :29-342.CA,N,C; matches 744 atoms
--------------------------------------------------------------------------------
3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------
begin time read from input coords = 0.150 ps
Number of triangulated 3-point waters found: 0
--------------------------------------------------------------------------------
4. RESULTS
--------------------------------------------------------------------------------
NSTEP = 1 TIME(PS) = 0.151 TEMP(K) = 28.05 PRESS =
0.0
Etot = 13530.8188 EKtot = 311.1434 EPtot =
13219.6754
BOND = 18079.7784 ANGLE = 2532.7846 DIHED =
2854.3092
1-4 NB = 1102.3720 1-4 EEL = 12507.0613 VDWAALS =
-1803.3055
EELEC = -19456.1610 EGB = -2597.1637 RESTRAINT =
0.0000
------------------------------------------------------------------------------
NSTEP = 2 TIME(PS) = 0.152 TEMP(K) = 50.91 PRESS =
0.0
Etot = 13535.2077 EKtot = 564.6577 EPtot =
12970.5500
BOND = 17830.6909 ANGLE = 2538.0818 DIHED =
2855.2943
1-4 NB = 1103.0046 1-4 EEL = 12505.4589 VDWAALS =
-1810.2193
EELEC = -19451.8318 EGB = -2600.0215 RESTRAINT =
0.0922
EAMBER (non-restraint) = 12970.4578
------------------------------------------------------------------------------
NSTEP = 3 TIME(PS) = 0.153 TEMP(K) = 90.78 PRESS =
0.0
Etot = 13536.9704 EKtot = 1006.8240 EPtot =
12530.1464
BOND = 17381.9019 ANGLE = 2555.8838 DIHED =
2857.2363
1-4 NB = 1104.3161 1-4 EEL = 12502.9748 VDWAALS =
-1823.0283
EELEC = -19446.4150 EGB = -2603.4940 RESTRAINT =
0.7709
EAMBER (non-restraint) = 12529.3755
------------------------------------------------------------------------------
NSTEP = 4 TIME(PS) = 0.154 TEMP(K) = 138.56 PRESS =
0.0
Etot = 13536.3288 EKtot = 1536.7385 EPtot =
11999.5903
BOND = 16822.8196 ANGLE = 2594.1698 DIHED =
2860.3778
1-4 NB = 1106.3535 1-4 EEL = 12499.7635 VDWAALS =
-1839.1626
EELEC = -19440.1814 EGB = -2607.4183 RESTRAINT =
2.8684
EAMBER (non-restraint) = 11996.7219
------------------------------------------------------------------------------
NSTEP = 5 TIME(PS) = 0.155 TEMP(K) = 184.56 PRESS =
0.0
Etot = 13535.5633 EKtot = 2046.9048 EPtot =
11488.6585
BOND = 16253.7773 ANGLE = 2658.0199 DIHED =
2864.9260
1-4 NB = 1109.1409 1-4 EEL = 12496.0225 VDWAALS =
-1855.5445
EELEC = -19433.4454 EGB = -2611.5444 RESTRAINT =
7.3063
EAMBER (non-restraint) = 11481.3522
------------------------------------------------------------------------------
NSTEP = 6 TIME(PS) = 0.156 TEMP(K) = 221.62 PRESS =
0.0
Etot = 13536.7252 EKtot = 2457.8332 EPtot =
11078.8919
BOND = 15753.5730 ANGLE = 2746.3712 DIHED =
2870.9625
1-4 NB = 1112.6725 1-4 EEL = 12491.9651 VDWAALS =
-1869.2906
EELEC = -19426.5413 EGB = -2615.6445 RESTRAINT =
14.8240
EAMBER (non-restraint) = 11064.0679
------------------------------------------------------------------------------
NSTEP = 7 TIME(PS) = 0.157 TEMP(K) = 247.35 PRESS =
0.0
Etot = 13540.6893 EKtot = 2743.2696 EPtot =
10797.4198
BOND = 15354.3889 ANGLE = 2851.9874 DIHED =
2878.4100
1-4 NB = 1116.9223 1-4 EEL = 12487.7933 VDWAALS =
-1878.6426
EELEC = -19419.8264 EGB = -2619.3921 RESTRAINT =
25.7790
EAMBER (non-restraint) = 10771.6408
------------------------------------------------------------------------------
NSTEP = 8 TIME(PS) = 0.158 TEMP(K) = 264.69 PRESS =
0.0
Etot = 13546.6479 EKtot = 2935.5284 EPtot =
10611.1195
BOND = 15034.9868 ANGLE = 2963.7003 DIHED =
2887.0548
1-4 NB = 1121.8618 1-4 EEL = 12483.6644 VDWAALS =
-1884.1463
EELEC = -19413.7002 EGB = -2622.3875 RESTRAINT =
40.0856
EAMBER (non-restraint) = 10571.0340
------------------------------------------------------------------------------
NSTEP = 9 TIME(PS) = 0.159 TEMP(K) = 280.07 PRESS =
0.0
Etot = 13552.2869 EKtot = 3106.1118 EPtot =
10446.1751
BOND = 14736.9039 ANGLE = 3069.6054 DIHED =
2896.6063
1-4 NB = 1127.4796 1-4 EEL = 12479.6591 VDWAALS =
-1888.5101
EELEC = -19408.5733 EGB = -2624.3037 RESTRAINT =
57.3078
EAMBER (non-restraint) = 10388.8673
------------------------------------------------------------------------------
NSTEP = 10 TIME(PS) = 0.160 TEMP(K) = 300.04 PRESS =
0.0
Etot = 13555.1046 EKtot = 3327.6258 EPtot =
10227.4788
BOND = 14396.7904 ANGLE = 3160.5024 DIHED =
2906.7961
1-4 NB = 1133.7874 1-4 EEL = 12475.7685 VDWAALS =
-1893.4800
EELEC = -19404.7164 EGB = -2624.8357 RESTRAINT =
76.8662
EAMBER (non-restraint) = 10150.6126
------------------------------------------------------------------------------
A V E R A G E S O V E R 10 S T E P S
NSTEP = 10 TIME(PS) = 0.160 TEMP(K) = 180.66 PRESS =
0.0
Etot = 13540.6343 EKtot = 2003.6637 EPtot =
11536.9706
BOND = 16164.5611 ANGLE = 2767.1107 DIHED =
2873.1973
1-4 NB = 1113.7911 1-4 EEL = 12493.0131 VDWAALS =
-1854.5330
EELEC = -19430.1392 EGB = -2612.6206 RESTRAINT =
22.5900
EAMBER (non-restraint) = 11514.3805
------------------------------------------------------------------------------
R M S F L U C T U A T I O N S
NSTEP = 10 TIME(PS) = 0.160 TEMP(K) = 93.44 PRESS =
0.0
Etot = 7.6164 EKtot = 1036.2851 EPtot =
1029.9500
BOND = 1250.2670 ANGLE = 220.5291 DIHED =
17.5095
1-4 NB = 10.3773 1-4 EEL = 10.4764 VDWAALS =
31.8828
EELEC = 17.3935 EGB = 9.7225 RESTRAINT =
25.7738
EAMBER (non-restraint) = 1004.1762
------------------------------------------------------------------------------
--------------------------------------------------------------------------------
5. TIMINGS
--------------------------------------------------------------------------------
| Read coords time 0.01 ( 0.04% of Total)
| Calc gb radii 3.22 (19.05% of Gen B)
| Calc gb diag 5.99 (35.49% of Gen B)
| Calc gb off-diag 7.68 (45.46% of Gen B)
| Gen Born time 16.89 (100.0% of Nonbo)
| Nonbond force 16.89 (99.79% of Force)
| Bond/Angle/Dihedral 0.04 ( 0.21% of Force)
| Force time 16.93 (99.56% of Runmd)
| Shake time 0.00 ( 0.01% of Runmd)
| Verlet update time 0.07 ( 0.42% of Runmd)
| Runmd Time 17.00 (99.38% of Total)
| Other 0.10 ( 0.58% of Total)
| Total time 17.11 (100.0% of ALL )
| Highest rstack allocated: 0
| Highest istack allocated: 0
| Job began at 21:52:14.420 on 01/05/2002
| Setup done at 21:52:14.526 on 01/05/2002
| Run done at 21:52:31.528 on 01/05/2002
| wallclock() was called 250 times
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
When I set nstlim=90 ,my output file is:
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
-------------------------------------------------------
Amber 9 SANDER 2006
-------------------------------------------------------
| Run on 01/05/2002 at 22:18:26
[-O]verwriting output
File Assignments:
| MDIN: equil.in
| MDOUT:
equil.out
|INPCRD:
heat6.rst
| PARM:
2RH1.prmtop
|RESTRT:
equil.rst
| REFC:
heat6.rst
| MDVEL:
mdvel
| MDEN:
mden
| MDCRD:
equil.mdcrd
|MDINFO:
mdinfo
|INPDIP:
inpdip
|RSTDIP:
rstdip
|INPTRA:
inptraj
|
Here is the input file:
Stage 2 equilibration 1
0-5ns
&cntrl
imin=0, irest=1,
ntx=5,
nstlim=90
,
dt=0.001,
ntc=2,
ntf=2,
ntt=1,
tautp=0.5,
tempi=300.0,
temp0=300.0,
ntpr=1,
ntwx=1,
ntb=0,igb=1,ntr=1,
restraintmask=':29-342.CA,N,C',
restraint_wt=10,
cut=999.,rgbmax=999.
/
--------------------------------------------------------------------------------
1. RESOURCE USE:
--------------------------------------------------------------------------------
|
Flags:
| New format PARM file being parsed.
| Version = 1.000 Date = 02/04/02 Time = 11:15:57
NATOM = 4475 NTYPES = 14 NBONH = 2257 MBONA = 2282
NTHETH = 5102 MTHETA = 3115 NPHIH = 9620 MPHIA = 7736
NHPARM = 0 NPARM = 0 NNB = 24804 NRES = 276
NBONA = 2282 NTHETA = 3115 NPHIA = 7736 NUMBND = 42
NUMANG = 89 NPTRA = 44 NATYP = 27 NPHB = 0
IFBOX = 0 NMXRS = 24 IFCAP = 0 NEXTRA = 0
NCOPY = 0
Implicit solvent radii are modified Bondi radii
(mbondi)
| Memory Use Allocated
| Real 251103
| Hollerith 27128
| Integer 252978
| Max Pairs 1
| nblistReal 0
| nblist Int 0
| Total 3055 kbytes
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals
--------------------------------------------------------------------------------
2. CONTROL DATA FOR THE RUN
--------------------------------------------------------------------------------
General flags:
imin = 0, nmropt = 0
Nature and format of input:
ntx = 5, irest = 1, ntrx = 1
Nature and format of output:
ntxo = 1, ntpr = 1, ntrx = 1, ntwr =
500
iwrap = 0, ntwx = 1, ntwv = 0, ntwe
= 0
ioutfm = 0, ntwprt = 0, idecomp = 0,
rbornstat= 0
Potential function:
ntf = 2, ntb = 0, igb = 1, nsnb
= 25
ipol = 0, gbsa = 0, iesp = 0
dielc = 1.00000, cut = 999.00000, intdiel = 1.00000
saltcon = 0.00000, offset = 0.09000, gbalpha= 1.00000
gbbeta = 0.00000, gbgamma = 0.00000, surften = 0.00500
rdt = 0.00000, rgbmax = 999.00000
alpb = 0
scnb = 2.00000, scee = 1.20000
Frozen or restrained atoms:
ibelly = 0, ntr = 1
Molecular dynamics:
nstlim = 90, nscm = 1000, nrespa = 1
t = 0.00000, dt = 0.00100, vlimit = 20.00000
Berendsen (weak-coupling) temperature regulation:
temp0 = 300.00000, tempi = 300.00000, tautp = 0.50000
SHAKE:
ntc = 2, jfastw = 0
tol = 0.00001
LOADING THE CONSTRAINED ATOMS AS GROUPS
5. REFERENCE ATOM COORDINATES
| INFO: Old style inpcrd file read
Mask :29-342.CA,N,C; matches 744 atoms
--------------------------------------------------------------------------------
3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------
begin time read from input coords = 0.150 ps
Number of triangulated 3-point waters found: 0
--------------------------------------------------------------------------------
4. RESULTS
--------------------------------------------------------------------------------
NSTEP = 1 TIME(PS) = 0.151 TEMP(K) = 28.05 PRESS =
0.0
Etot = 13530.8188 EKtot = 311.1434 EPtot =
13219.6754
BOND = 18079.7784 ANGLE = 2532.7846 DIHED =
2854.3092
1-4 NB = 1102.3720 1-4 EEL = 12507.0613 VDWAALS =
-1803.3055
EELEC = -19456.1610 EGB = -2597.1637 RESTRAINT =
0.0000
------------------------------------------------------------------------------
NSTEP = 2 TIME(PS) = 0.152 TEMP(K) = 50.91 PRESS =
0.0
Etot = 13535.2077 EKtot = 564.6577 EPtot =
12970.5500
BOND = 17830.6909 ANGLE = 2538.0818 DIHED =
2855.2943
1-4 NB = 1103.0046 1-4 EEL = 12505.4589 VDWAALS =
-1810.2193
EELEC = -19451.8318 EGB = -2600.0215 RESTRAINT =
0.0922
EAMBER (non-restraint) = 12970.4578
------------------------------------------------------------------------------
NSTEP = 3 TIME(PS) = 0.153 TEMP(K) = 90.78 PRESS =
0.0
Etot = 13536.9704 EKtot = 1006.8240 EPtot =
12530.1464
BOND = 17381.9019 ANGLE = 2555.8838 DIHED =
2857.2363
1-4 NB = 1104.3161 1-4 EEL = 12502.9748 VDWAALS =
-1823.0283
EELEC = -19446.4150 EGB = -2603.4940 RESTRAINT =
0.7709
EAMBER (non-restraint) = 12529.3755
------------------------------------------------------------------------------
NSTEP = 4 TIME(PS) = 0.154 TEMP(K) = 138.56 PRESS =
0.0
Etot = 13536.3288 EKtot = 1536.7385 EPtot =
11999.5903
BOND = 16822.8196 ANGLE = 2594.1698 DIHED =
2860.3778
1-4 NB = 1106.3535 1-4 EEL = 12499.7635 VDWAALS =
-1839.1626
EELEC = -19440.1814 EGB = -2607.4183 RESTRAINT =
2.8684
EAMBER (non-restraint) = 11996.7219
------------------------------------------------------------------------------
NSTEP = 5 TIME(PS) = 0.155 TEMP(K) = 184.56 PRESS =
0.0
Etot = 13535.5633 EKtot = 2046.9048 EPtot =
11488.6585
BOND = 16253.7773 ANGLE = 2658.0199 DIHED =
2864.9260
1-4 NB = 1109.1409 1-4 EEL = 12496.0225 VDWAALS =
-1855.5445
EELEC = -19433.4454 EGB = -2611.5444 RESTRAINT =
7.3063
EAMBER (non-restraint) = 11481.3522
------------------------------------------------------------------------------
NSTEP = 6 TIME(PS) = 0.156 TEMP(K) = 221.62 PRESS =
0.0
Etot = 13536.7252 EKtot = 2457.8332 EPtot =
11078.8919
BOND = 15753.5730 ANGLE = 2746.3712 DIHED =
2870.9625
1-4 NB = 1112.6725 1-4 EEL = 12491.9651 VDWAALS =
-1869.2906
EELEC = -19426.5413 EGB = -2615.6445 RESTRAINT =
14.8240
EAMBER (non-restraint) = 11064.0679
------------------------------------------------------------------------------
NSTEP = 7 TIME(PS) = 0.157 TEMP(K) = 247.35 PRESS =
0.0
Etot = 13540.6893 EKtot = 2743.2696 EPtot =
10797.4198
BOND = 15354.3889 ANGLE = 2851.9874 DIHED =
2878.4100
1-4 NB = 1116.9223 1-4 EEL = 12487.7933 VDWAALS =
-1878.6426
EELEC = -19419.8264 EGB = -2619.3921 RESTRAINT =
25.7790
EAMBER (non-restraint) = 10771.6408
------------------------------------------------------------------------------
NSTEP = 8 TIME(PS) = 0.158 TEMP(K) = 264.69 PRESS =
0.0
Etot = 13546.6479 EKtot = 2935.5284 EPtot =
10611.1195
BOND = 15034.9868 ANGLE = 2963.7003 DIHED =
2887.0548
1-4 NB = 1121.8618 1-4 EEL = 12483.6644 VDWAALS =
-1884.1463
EELEC = -19413.7002 EGB = -2622.3875 RESTRAINT =
40.0856
EAMBER (non-restraint) = 10571.0340
------------------------------------------------------------------------------
NSTEP = 9 TIME(PS) = 0.159 TEMP(K) = 280.07 PRESS =
0.0
Etot = 13552.2869 EKtot = 3106.1118 EPtot =
10446.1751
BOND = 14736.9039 ANGLE = 3069.6054 DIHED =
2896.6063
1-4 NB = 1127.4796 1-4 EEL = 12479.6591 VDWAALS =
-1888.5101
EELEC = -19408.5733 EGB = -2624.3037 RESTRAINT =
57.3078
EAMBER (non-restraint) = 10388.8673
------------------------------------------------------------------------------
NSTEP = 10 TIME(PS) = 0.160 TEMP(K) = 300.04 PRESS =
0.0
Etot = 13555.1046 EKtot = 3327.6258 EPtot =
10227.4788
BOND = 14396.7904 ANGLE = 3160.5024 DIHED =
2906.7961
1-4 NB = 1133.7874 1-4 EEL = 12475.7685 VDWAALS =
-1893.4800
EELEC = -19404.7164 EGB = -2624.8357 RESTRAINT =
76.8662
EAMBER (non-restraint) = 10150.6126
------------------------------------------------------------------------------
NSTEP = 11 TIME(PS) = 0.161 TEMP(K) = 327.90 PRESS =
0.0
Etot = 13553.9107 EKtot = 3636.5944 EPtot =
9917.3163
BOND = 13979.2577 ANGLE = 3232.8984 DIHED =
2917.5014
1-4 NB = 1140.8008 1-4 EEL = 12471.9077 VDWAALS =
-1897.4490
EELEC = -19402.0786 EGB = -2623.7922 RESTRAINT =
98.2700
EAMBER (non-restraint) = 9819.0463
------------------------------------------------------------------------------
NSTEP = 12 TIME(PS) = 0.162 TEMP(K) = 362.22 PRESS =
0.0
Etot = 13549.2018 EKtot = 4017.1980 EPtot =
9532.0038
BOND = 13494.2937 ANGLE = 3290.4142 DIHED =
2928.7545
1-4 NB = 1148.4914 1-4 EEL = 12467.9539 VDWAALS =
-1897.6055
EELEC = -19400.2912 EGB = -2621.2917 RESTRAINT =
121.2846
EAMBER (non-restraint) = 9410.7193
------------------------------------------------------------------------------
NSTEP = 13 TIME(PS) = 0.163 TEMP(K) = 397.80 PRESS =
0.0
Etot = 13542.9831 EKtot = 4411.8186 EPtot =
9131.1645
BOND = 12990.7125 ANGLE = 3342.0769 DIHED =
2940.6183
1-4 NB = 1156.7487 1-4 EEL = 12463.7978 VDWAALS =
-1892.1592
EELEC = -19398.8429 EGB = -2617.7673 RESTRAINT =
145.9797
EAMBER (non-restraint) = 8985.1848
------------------------------------------------------------------------------
NSTEP = 14 TIME(PS) = 0.164 TEMP(K) = 428.49 PRESS =
0.0
Etot = 13537.8256 EKtot = 4752.2259 EPtot =
8785.5998
BOND = 12529.0539 ANGLE = 3397.5726 DIHED =
2953.0856
1-4 NB = 1165.4374 1-4 EEL = 12459.4071 VDWAALS =
-1880.5340
EELEC = -19397.2203 EGB = -2613.8613 RESTRAINT =
172.6588
EAMBER (non-restraint) = 8612.9410
------------------------------------------------------------------------------
NSTEP = 15 TIME(PS) = 0.165 TEMP(K) = 450.50 PRESS =
0.0
Etot = 13535.4206 EKtot = 4996.2954 EPtot =
8539.1252
BOND = 12149.0817 ANGLE = 3461.9504 DIHED =
2966.0236
1-4 NB = 1174.5142 1-4 EEL = 12454.8812 VDWAALS =
-1863.8483
EELEC = -19394.9556 EGB = -2610.2463 RESTRAINT =
201.7243
EAMBER (non-restraint) = 8337.4008
------------------------------------------------------------------------------
NSTEP = 16 TIME(PS) = 0.166 TEMP(K) = 464.39 PRESS =
0.0
Etot = 13535.4842 EKtot = 5150.2829 EPtot =
8385.2012
BOND = 11849.8349 ANGLE = 3533.3869 DIHED =
2979.2392
1-4 NB = 1183.5979 1-4 EEL = 12450.4392 VDWAALS =
-1845.6535
EELEC = -19391.6369 EGB = -2607.5706 RESTRAINT =
233.5641
EAMBER (non-restraint) = 8151.6371
------------------------------------------------------------------------------
NSTEP = 17 TIME(PS) = 0.167 TEMP(K) = 474.46 PRESS =
0.0
Etot = 13535.7953 EKtot = 5262.0076 EPtot =
8273.7877
BOND = 11591.1050 ANGLE = 3607.5974 DIHED =
2992.6376
1-4 NB = 1191.0760 1-4 EEL = 12446.3119 VDWAALS =
-1830.3370
EELEC = -19386.9343 EGB = -2606.1791 RESTRAINT =
268.5103
EAMBER (non-restraint) = 8005.2774
------------------------------------------------------------------------------
NSTEP = 18 TIME(PS) = 0.168 TEMP(K) = 485.80 PRESS =
0.0
Etot = 13534.1645 EKtot = 5387.7900 EPtot =
8146.3745
BOND = 11316.7056 ANGLE = 3685.3416 DIHED =
3006.0780
1-4 NB = 1196.0218 1-4 EEL = 12442.6270 VDWAALS =
-1820.2622
EELEC = -19380.6751 EGB = -2606.3202 RESTRAINT =
306.8580
EAMBER (non-restraint) = 7839.5165
------------------------------------------------------------------------------
NSTEP = 19 TIME(PS) = 0.169 TEMP(K) = 501.61 PRESS =
0.0
Etot = 13530.5024 EKtot = 5563.0951 EPtot =
7967.4073
BOND = 10993.4348 ANGLE = 3763.0250 DIHED =
3019.2754
1-4 NB = 1199.9557 1-4 EEL = 12439.3455 VDWAALS =
-1815.5349
EELEC = -19372.9525 EGB = -2608.0353 RESTRAINT =
348.8938
EAMBER (non-restraint) = 7618.5135
------------------------------------------------------------------------------
NSTEP = 20 TIME(PS) = 0.170 TEMP(K) = 522.55 PRESS =
0.0
Etot = 13524.4671 EKtot = 5795.3694 EPtot =
7729.0977
BOND = 10630.2474 ANGLE = 3822.3208 DIHED =
3032.0470
1-4 NB = 1203.7097 1-4 EEL = 12436.2650 VDWAALS =
-1815.1375
EELEC = -19364.0375 EGB = -2611.2055 RESTRAINT =
394.8884
EAMBER (non-restraint) = 7334.2093
------------------------------------------------------------------------------
NSTEP = 21 TIME(PS) = 0.171 TEMP(K) = 546.95 PRESS =
0.0
Etot = 13516.3756 EKtot = 6065.9260 EPtot =
7450.4496
BOND = 10256.6499 ANGLE = 3853.9778 DIHED =
3044.1356
1-4 NB = 1204.7703 1-4 EEL = 12433.0639 VDWAALS =
-1817.6994
EELEC = -19353.9228 EGB = -2615.5996 RESTRAINT =
445.0739
EAMBER (non-restraint) = 7005.3756
------------------------------------------------------------------------------
NSTEP = 22 TIME(PS) = 0.172 TEMP(K) = 571.34 PRESS =
0.0
Etot = 13507.5295 EKtot = 6336.4310 EPtot =
7171.0986
BOND = 9901.4138 ANGLE = 3869.3176 DIHED =
3055.8223
1-4 NB = 1201.1159 1-4 EEL = 12429.3011 VDWAALS =
-1822.2615
EELEC = -19342.4390 EGB = -2620.7867 RESTRAINT =
499.6150
EAMBER (non-restraint) = 6671.4835
------------------------------------------------------------------------------
NSTEP = 23 TIME(PS) = 0.173 TEMP(K) = 592.04 PRESS =
0.0
Etot = 13499.9282 EKtot = 6566.0638 EPtot =
6933.8644
BOND = 9585.8379 ANGLE = 3886.8736 DIHED =
3067.9339
1-4 NB = 1194.1813 1-4 EEL = 12424.4725 VDWAALS =
-1827.9780
EELEC = -19329.7664 EGB = -2626.2511 RESTRAINT =
558.5606
EAMBER (non-restraint) = 6375.3038
------------------------------------------------------------------------------
NSTEP = 24 TIME(PS) = 0.174 TEMP(K) = 606.86 PRESS =
0.0
Etot = 13493.4596 EKtot = 6730.3993 EPtot =
6763.0603
BOND = 9319.8316 ANGLE = 3919.4310 DIHED =
3079.8337
1-4 NB = 1184.6692 1-4 EEL = 12418.1273 VDWAALS =
-1832.8412
EELEC = -19316.3168 EGB = -2631.4800 RESTRAINT =
621.8054
EAMBER (non-restraint) = 6141.2549
------------------------------------------------------------------------------
NSTEP = 25 TIME(PS) = 0.175 TEMP(K) = 615.51 PRESS =
0.0
Etot = 13487.8896 EKtot = 6826.2713 EPtot =
6661.6183
BOND = 9100.2495 ANGLE = 3969.1243 DIHED =
3091.9258
1-4 NB = 1173.8906 1-4 EEL = 12409.9434 VDWAALS =
-1834.0259
EELEC = -19302.4573 EGB = -2636.1220 RESTRAINT =
689.0899
EAMBER (non-restraint) = 5972.5284
------------------------------------------------------------------------------
NSTEP = 26 TIME(PS) = 0.176 TEMP(K) = 619.14 PRESS =
0.0
Etot = 13481.4169 EKtot = 6866.5408 EPtot =
6614.8760
BOND = 8913.9310 ANGLE = 4029.4329 DIHED =
3104.1461
1-4 NB = 1165.6665 1-4 EEL = 12400.0727 VDWAALS =
-1829.8875
EELEC = -19288.4739 EGB = -2640.0342 RESTRAINT =
760.0223
EAMBER (non-restraint) = 5854.8537
------------------------------------------------------------------------------
NSTEP = 27 TIME(PS) = 0.177 TEMP(K) = 616.43 PRESS =
0.0
Etot = 13466.3083 EKtot = 6836.4888 EPtot =
6629.8195
BOND = 8743.4378 ANGLE = 4088.8511 DIHED =
3114.7393
1-4 NB = 1198.1725 1-4 EEL = 12389.2233 VDWAALS =
-1820.7647
EELEC = -19274.6031 EGB = -2643.3483 RESTRAINT =
834.1116
EAMBER (non-restraint) = 5795.7079
------------------------------------------------------------------------------
NSTEP = 28 TIME(PS) = 0.178 TEMP(K) = 619.49 PRESS =
0.0
Etot = 13455.9147 EKtot = 6870.4261 EPtot =
6585.4885
BOND = 8571.7316 ANGLE = 4127.7195 DIHED =
3123.0576
1-4 NB = 1188.8680 1-4 EEL = 12377.9449 VDWAALS =
-1807.4575
EELEC = -19260.9421 EGB = -2646.2957 RESTRAINT =
910.8622
EAMBER (non-restraint) = 5674.6264
------------------------------------------------------------------------------
NSTEP = 29 TIME(PS) = 0.179 TEMP(K) = 629.62 PRESS =
0.0
Etot = 13462.3445 EKtot = 6982.8060 EPtot =
6479.5386
BOND = 8383.8442 ANGLE = 4136.6195 DIHED =
3129.2275
1-4 NB = 1162.3260 1-4 EEL = 12365.6052 VDWAALS =
-1791.4985
EELEC = -19247.4172 EGB = -2648.9035 RESTRAINT =
989.7353
EAMBER (non-restraint) = 5489.8032
------------------------------------------------------------------------------
NSTEP = 30 TIME(PS) = 0.180 TEMP(K) = 642.33 PRESS =
0.0
Etot = 13449.5437 EKtot = 7123.8234 EPtot =
6325.7203
BOND = 8169.8723 ANGLE = 4110.9209 DIHED =
3135.5660
1-4 NB = 1149.1393 1-4 EEL = 12349.8009 VDWAALS =
-1775.0516
EELEC = -19233.9697 EGB = -2650.7566 RESTRAINT =
1070.1988
EAMBER (non-restraint) = 5255.5216
------------------------------------------------------------------------------
NSTEP = 31 TIME(PS) = 0.181 TEMP(K) = 658.71 PRESS =
0.0
Etot = 13440.0606 EKtot = 7305.4892 EPtot =
6134.5714
BOND = 7929.6714 ANGLE = 4063.6411 DIHED =
3142.8984
1-4 NB = 1144.3485 1-4 EEL = 12332.6114 VDWAALS =
-1757.8547
EELEC = -19220.7363 EGB = -2651.8867 RESTRAINT =
1151.8783
EAMBER (non-restraint) = 4982.6931
------------------------------------------------------------------------------
NSTEP = 32 TIME(PS) = 0.182 TEMP(K) = 675.01 PRESS =
0.0
Etot = 13427.8628 EKtot = 7486.1562 EPtot =
5941.7066
BOND = 7675.1891 ANGLE = 4017.1106 DIHED =
3149.9243
1-4 NB = 1144.3651 1-4 EEL = 12315.6532 VDWAALS =
-1735.0461
EELEC = -19207.7684 EGB = -2652.3719 RESTRAINT =
1234.6507
EAMBER (non-restraint) = 4707.0559
------------------------------------------------------------------------------
NSTEP = 33 TIME(PS) = 0.183 TEMP(K) = 688.32 PRESS =
0.0
Etot = 13419.7475 EKtot = 7633.8360 EPtot =
5785.9115
BOND = 7428.7810 ANGLE = 3989.1087 DIHED =
3157.3321
1-4 NB = 1146.1181 1-4 EEL = 12299.4920 VDWAALS =
-1706.1109
EELEC = -19195.1210 EGB = -2652.3923 RESTRAINT =
1318.7039
EAMBER (non-restraint) = 4467.2076
------------------------------------------------------------------------------
NSTEP = 34 TIME(PS) = 0.184 TEMP(K) = 697.99 PRESS =
0.0
Etot = 13406.7794 EKtot = 7741.0360 EPtot =
5665.7434
BOND = 7213.1620 ANGLE = 3989.3043 DIHED =
3165.2679
1-4 NB = 1152.7048 1-4 EEL = 12284.3383 VDWAALS =
-1708.3488
EELEC = -19182.7950 EGB = -2652.2625 RESTRAINT =
1404.3725
EAMBER (non-restraint) = 4261.3709
------------------------------------------------------------------------------
NSTEP = 35 TIME(PS) = 0.185 TEMP(K) = 700.63 PRESS =
0.0
Etot = 13398.7038 EKtot = 7770.3379 EPtot =
5628.3659
BOND = 7038.9303 ANGLE = 4024.1493 DIHED =
3173.7793
1-4 NB = 1169.3553 1-4 EEL = 12270.5029 VDWAALS =
-1717.2882
EELEC = -19170.6525 EGB = -2652.3351 RESTRAINT =
1491.9246
EAMBER (non-restraint) = 4136.4413
------------------------------------------------------------------------------
NSTEP = 36 TIME(PS) = 0.186 TEMP(K) = 696.75 PRESS =
0.0
Etot = 13398.0296 EKtot = 7727.3659 EPtot =
5670.6638
BOND = 6900.7391 ANGLE = 4083.3696 DIHED =
3183.5753
1-4 NB = 1192.8106 1-4 EEL = 12258.3216 VDWAALS =
-1717.8907
EELEC = -19158.5270 EGB = -2653.2096 RESTRAINT =
1581.4748
EAMBER (non-restraint) = 4089.1890
------------------------------------------------------------------------------
NSTEP = 37 TIME(PS) = 0.187 TEMP(K) = 693.98 PRESS =
0.0
Etot = 13380.2176 EKtot = 7696.6321 EPtot =
5683.5855
BOND = 6782.6517 ANGLE = 4120.6275 DIHED =
3192.8471
1-4 NB = 1181.5658 1-4 EEL = 12247.7346 VDWAALS =
-1713.4026
EELEC = -19146.3760 EGB = -2655.0708 RESTRAINT =
1673.0081
EAMBER (non-restraint) = 4010.5774
------------------------------------------------------------------------------
NSTEP = 38 TIME(PS) = 0.188 TEMP(K) = 690.68 PRESS =
0.0
Etot = 13374.2007 EKtot = 7660.0390 EPtot =
5714.1617
BOND = 6670.0098 ANGLE = 4146.2340 DIHED =
3204.5482
1-4 NB = 1183.2731 1-4 EEL = 12238.2316 VDWAALS =
-1702.6044
EELEC = -19134.4098 EGB = -2657.5874 RESTRAINT =
1766.4666
EAMBER (non-restraint) = 3947.6951
------------------------------------------------------------------------------
NSTEP = 39 TIME(PS) = 0.189 TEMP(K) = 687.05 PRESS =
0.0
Etot = 13367.7785 EKtot = 7619.6989 EPtot =
5748.0796
BOND = 6547.7682 ANGLE = 4161.7289 DIHED =
3218.9521
1-4 NB = 1198.1836 1-4 EEL = 12230.0951 VDWAALS =
-1686.8819
EELEC = -19122.8327 EGB = -2660.5988 RESTRAINT =
1861.6649
EAMBER (non-restraint) = 3886.4146
------------------------------------------------------------------------------
NSTEP = 40 TIME(PS) = 0.190 TEMP(K) = 686.50 PRESS =
0.0
Etot = 13360.0505 EKtot = 7613.6714 EPtot =
5746.3791
BOND = 6407.9531 ANGLE = 4153.7556 DIHED =
3236.1419
1-4 NB = 1211.5160 1-4 EEL = 12223.4585 VDWAALS =
-1669.3092
EELEC = -19111.6460 EGB = -2663.9068 RESTRAINT =
1958.4162
EAMBER (non-restraint) = 3787.9629
------------------------------------------------------------------------------
NSTEP = 41 TIME(PS) = 0.191 TEMP(K) = 690.07 PRESS =
0.0
Etot = 13348.3456 EKtot = 7653.2087 EPtot =
5695.1369
BOND = 6252.4336 ANGLE = 4123.1693 DIHED =
3254.4110
1-4 NB = 1211.0276 1-4 EEL = 12218.3161 VDWAALS =
-1652.8054
EELEC = -19100.7599 EGB = -2667.2473 RESTRAINT =
2056.5919
EAMBER (non-restraint) = 3638.5450
------------------------------------------------------------------------------
NSTEP = 42 TIME(PS) = 0.192 TEMP(K) = 694.95 PRESS =
0.0
Etot = 13336.7714 EKtot = 7707.3059 EPtot =
5629.4655
BOND = 6092.5603 ANGLE = 4086.4960 DIHED =
3271.8721
1-4 NB = 1209.6205 1-4 EEL = 12214.4271 VDWAALS =
-1640.3374
EELEC = -19090.5725 EGB = -2670.7138 RESTRAINT =
2156.1132
EAMBER (non-restraint) = 3473.3523
------------------------------------------------------------------------------
NSTEP = 43 TIME(PS) = 0.193 TEMP(K) = 697.73 PRESS =
0.0
Etot = 13325.5721 EKtot = 7738.2408 EPtot =
5587.3313
BOND = 5945.2028 ANGLE = 4063.5464 DIHED =
3287.3137
1-4 NB = 1212.1213 1-4 EEL = 12211.3003 VDWAALS =
-1632.5142
EELEC = -19082.1713 EGB = -2674.3594 RESTRAINT =
2256.8916
EAMBER (non-restraint) = 3330.4397
------------------------------------------------------------------------------
NSTEP = 44 TIME(PS) = 0.194 TEMP(K) = 696.63 PRESS =
0.0
Etot = 13318.0012 EKtot = 7725.9674 EPtot =
5592.0338
BOND = 5824.7899 ANGLE = 4067.3298 DIHED =
3300.3907
1-4 NB = 1215.4174 1-4 EEL = 12208.3436 VDWAALS =
-1629.0904
EELEC = -19075.6299 EGB = -2678.2433 RESTRAINT =
2358.7260
EAMBER (non-restraint) = 3233.3078
------------------------------------------------------------------------------
NSTEP = 45 TIME(PS) = 0.195 TEMP(K) = 691.84 PRESS =
0.0
Etot = 13305.1906 EKtot = 7672.8280 EPtot =
5632.3626
BOND = 5734.0793 ANGLE = 4098.2030 DIHED =
3311.0820
1-4 NB = 1224.3974 1-4 EEL = 12205.0424 VDWAALS =
-1649.5517
EELEC = -19069.8460 EGB = -2682.2444 RESTRAINT =
2461.2005
EAMBER (non-restraint) = 3171.1621
------------------------------------------------------------------------------
NSTEP = 46 TIME(PS) = 0.196 TEMP(K) = 683.45 PRESS =
0.0
Etot = 13312.6175 EKtot = 7579.8308 EPtot =
5732.7866
BOND = 5660.7039 ANGLE = 4143.7784 DIHED =
3319.1632
1-4 NB = 1281.7901 1-4 EEL = 12201.3616 VDWAALS =
-1686.9997
EELEC = -19064.4831 EGB = -2686.0878 RESTRAINT =
2563.5601
EAMBER (non-restraint) = 3169.2266
------------------------------------------------------------------------------
NSTEP = 47 TIME(PS) = 0.197 TEMP(K) = 684.13 PRESS =
0.0
Etot = 13288.6716 EKtot = 7587.3568 EPtot =
5701.3147
BOND = 5580.5070 ANGLE = 4172.4525 DIHED =
3323.2445
1-4 NB = 1227.2889 1-4 EEL = 12198.7403 VDWAALS =
-1715.8351
EELEC = -19059.9329 EGB = -2689.7265 RESTRAINT =
2664.5761
EAMBER (non-restraint) = 3036.7386
------------------------------------------------------------------------------
NSTEP = 48 TIME(PS) = 0.198 TEMP(K) = 687.86 PRESS =
0.0
Etot = 13280.2263 EKtot = 7628.7276 EPtot =
5651.4987
BOND = 5481.0609 ANGLE = 4172.1390 DIHED =
3324.3415
1-4 NB = 1195.1156 1-4 EEL = 12196.0253 VDWAALS =
-1733.1727
EELEC = -19055.9843 EGB = -2692.7564 RESTRAINT =
2764.7298
EAMBER (non-restraint) = 2886.7689
------------------------------------------------------------------------------
NSTEP = 49 TIME(PS) = 0.199 TEMP(K) = 690.42 PRESS =
0.0
Etot = 13274.2761 EKtot = 7657.1237 EPtot =
5617.1524
BOND = 5357.4994 ANGLE = 4168.6881 DIHED =
3325.0226
1-4 NB = 1198.1043 1-4 EEL = 12192.2669 VDWAALS =
-1741.0053
EELEC = -19052.4105 EGB = -2695.2712 RESTRAINT =
2864.2583
EAMBER (non-restraint) = 2752.8942
------------------------------------------------------------------------------
NSTEP = 50 TIME(PS) = 0.200 TEMP(K) = 695.29 PRESS =
0.0
Etot = 13266.9706 EKtot = 7711.1714 EPtot =
5555.7993
BOND = 5209.1438 ANGLE = 4171.4641 DIHED =
3325.2592
1-4 NB = 1190.0741 1-4 EEL = 12187.3635 VDWAALS =
-1744.5171
EELEC = -19048.5496 EGB = -2697.3703 RESTRAINT =
2962.9315
EAMBER (non-restraint) = 2592.8678
------------------------------------------------------------------------------
NSTEP = 51 TIME(PS) = 0.201 TEMP(K) = 703.09 PRESS =
0.0
Etot = 13253.6223 EKtot = 7797.6317 EPtot =
5455.9906
BOND = 5043.0289 ANGLE = 4175.5727 DIHED =
3325.9819
1-4 NB = 1162.3364 1-4 EEL = 12181.5621 VDWAALS =
-1750.1418
EELEC = -19043.7678 EGB = -2699.2456 RESTRAINT =
3060.6636
EAMBER (non-restraint) = 2395.3269
------------------------------------------------------------------------------
NSTEP = 52 TIME(PS) = 0.202 TEMP(K) = 709.56 PRESS =
0.0
Etot = 13244.0267 EKtot = 7869.3583 EPtot =
5374.6684
BOND = 4872.1738 ANGLE = 4185.3535 DIHED =
3327.0658
1-4 NB = 1147.5118 1-4 EEL = 12175.1003 VDWAALS =
-1751.4443
EELEC = -19037.7579 EGB = -2700.9417 RESTRAINT =
3157.6070
EAMBER (non-restraint) = 2217.0613
------------------------------------------------------------------------------
NSTEP = 53 TIME(PS) = 0.203 TEMP(K) = 712.53 PRESS =
0.0
Etot = 13234.0042 EKtot = 7902.3385 EPtot =
5331.6658
BOND = 4711.9386 ANGLE = 4201.0659 DIHED =
3327.5906
1-4 NB = 1142.9650 1-4 EEL = 12168.3487 VDWAALS =
-1740.9778
EELEC = -19030.9100 EGB = -2702.4872 RESTRAINT =
3254.1319
EAMBER (non-restraint) = 2077.5338
------------------------------------------------------------------------------
NSTEP = 54 TIME(PS) = 0.204 TEMP(K) = 710.88 PRESS =
0.0
Etot = 13222.4727 EKtot = 7884.0595 EPtot =
5338.4132
BOND = 4575.4889 ANGLE = 4215.8830 DIHED =
3326.2054
1-4 NB = 1156.5543 1-4 EEL = 12161.6462 VDWAALS =
-1720.2968
EELEC = -19023.9875 EGB = -2703.8325 RESTRAINT =
3350.7523
EAMBER (non-restraint) = 1987.6609
------------------------------------------------------------------------------
NSTEP = 55 TIME(PS) = 0.205 TEMP(K) = 704.65 PRESS =
0.0
Etot = 13216.0829 EKtot = 7814.9718 EPtot =
5401.1111
BOND = 4469.9629 ANGLE = 4225.6875 DIHED =
3320.9323
1-4 NB = 1199.1915 1-4 EEL = 12155.1163 VDWAALS =
-1695.5037
EELEC = -19017.4404 EGB = -2704.9709 RESTRAINT =
3448.1355
EAMBER (non-restraint) = 1952.9756
------------------------------------------------------------------------------
NSTEP = 56 TIME(PS) = 0.206 TEMP(K) = 698.54 PRESS =
0.0
Etot = 13214.6081 EKtot = 7747.1758 EPtot =
5467.4323
BOND = 4393.6481 ANGLE = 4222.8624 DIHED =
3313.9091
1-4 NB = 1230.5540 1-4 EEL = 12148.6695 VDWAALS =
-1672.0081
EELEC = -19011.2147 EGB = -2706.0580 RESTRAINT =
3547.0701
EAMBER (non-restraint) = 1920.3622
------------------------------------------------------------------------------
NSTEP = 57 TIME(PS) = 0.207 TEMP(K) = 697.62 PRESS =
0.0
Etot = 13201.5854 EKtot = 7736.9847 EPtot =
5464.6008
BOND = 4338.0188 ANGLE = 4198.5266 DIHED =
3307.4603
1-4 NB = 1196.9658 1-4 EEL = 12142.2604 VDWAALS =
-1654.1037
EELEC = -19005.0394 EGB = -2707.4308 RESTRAINT =
3647.9427
EAMBER (non-restraint) = 1816.6581
------------------------------------------------------------------------------
NSTEP = 58 TIME(PS) = 0.208 TEMP(K) = 698.17 PRESS =
0.0
Etot = 13188.9915 EKtot = 7743.0858 EPtot =
5445.9057
BOND = 4293.7963 ANGLE = 4153.3135 DIHED =
3299.7692
1-4 NB = 1164.1567 1-4 EEL = 12136.3192 VDWAALS =
-1643.4340
EELEC = -18998.8821 EGB = -2709.3864 RESTRAINT =
3750.2532
EAMBER (non-restraint) = 1695.6525
------------------------------------------------------------------------------
NSTEP = 59 TIME(PS) = 0.209 TEMP(K) = 696.11 PRESS =
0.0
Etot = 13180.8303 EKtot = 7720.1844 EPtot =
5460.6459
BOND = 4248.9183 ANGLE = 4099.9116 DIHED =
3291.3154
1-4 NB = 1168.0875 1-4 EEL = 12131.6534 VDWAALS =
-1627.7438
EELEC = -18992.7829 EGB = -2711.9781 RESTRAINT =
3853.2646
EAMBER (non-restraint) = 1607.3813
------------------------------------------------------------------------------
NSTEP = 60 TIME(PS) = 0.210 TEMP(K) = 692.79 PRESS =
0.0
Etot = 13181.6746 EKtot = 7683.3717 EPtot =
5498.3029
BOND = 4191.5123 ANGLE = 4058.9900 DIHED =
3282.5316
1-4 NB = 1181.6853 1-4 EEL = 12129.1660 VDWAALS =
-1600.3151
EELEC = -18986.5045 EGB = -2715.1900 RESTRAINT =
3956.4273
EAMBER (non-restraint) = 1541.8756
------------------------------------------------------------------------------
NSTEP = 61 TIME(PS) = 0.211 TEMP(K) = 695.95 PRESS =
0.0
Etot = 13161.1216 EKtot = 7718.4833 EPtot =
5442.6383
BOND = 4114.5621 ANGLE = 4042.1365 DIHED =
3274.7528
1-4 NB = 1179.3509 1-4 EEL = 12130.1488 VDWAALS =
-1658.4754
EELEC = -18980.2755 EGB = -2718.8625 RESTRAINT =
4059.3006
EAMBER (non-restraint) = 1383.3377
------------------------------------------------------------------------------
NSTEP = 62 TIME(PS) = 0.212 TEMP(K) = 698.57 PRESS =
0.0
Etot = 13151.9946 EKtot = 7747.4946 EPtot =
5404.5000
BOND = 4019.6437 ANGLE = 4042.5915 DIHED =
3268.3785
1-4 NB = 1162.6174 1-4 EEL = 12134.1492 VDWAALS =
-1687.6736
EELEC = -18973.8515 EGB = -2722.9589 RESTRAINT =
4161.6037
EAMBER (non-restraint) = 1242.8964
------------------------------------------------------------------------------
NSTEP = 63 TIME(PS) = 0.213 TEMP(K) = 698.15 PRESS =
0.0
Etot = 13140.9338 EKtot = 7742.8764 EPtot =
5398.0573
BOND = 3918.2147 ANGLE = 4067.4542 DIHED =
3266.4956
1-4 NB = 1143.5156 1-4 EEL = 12140.0110 VDWAALS =
-1705.5524
EELEC = -18967.8499 EGB = -2727.3740 RESTRAINT =
4263.1425
EAMBER (non-restraint) = 1134.9148
------------------------------------------------------------------------------
NSTEP = 64 TIME(PS) = 0.214 TEMP(K) = 692.78 PRESS =
0.0
Etot = 13133.3897 EKtot = 7683.2867 EPtot =
5450.1030
BOND = 3827.4262 ANGLE = 4123.4953 DIHED =
3269.3668
1-4 NB = 1132.1940 1-4 EEL = 12146.1035 VDWAALS =
-1716.9354
EELEC = -18963.4504 EGB = -2731.8123 RESTRAINT =
4363.7154
EAMBER (non-restraint) = 1086.3876
------------------------------------------------------------------------------
NSTEP = 65 TIME(PS) = 0.215 TEMP(K) = 683.45 PRESS =
0.0
Etot = 13125.4631 EKtot = 7579.8104 EPtot =
5545.6526
BOND = 3761.9028 ANGLE = 4192.5824 DIHED =
3277.7298
1-4 NB = 1118.5117 1-4 EEL = 12150.8788 VDWAALS =
-1722.1073
EELEC = -18960.8535 EGB = -2735.8949 RESTRAINT =
4462.9028
EAMBER (non-restraint) = 1082.7498
------------------------------------------------------------------------------
NSTEP = 66 TIME(PS) = 0.216 TEMP(K) = 671.91 PRESS =
0.0
Etot = 13120.6492 EKtot = 7451.8441 EPtot =
5668.8051
BOND = 3727.1506 ANGLE = 4245.4661 DIHED =
3295.0827
1-4 NB = 1106.4096 1-4 EEL = 12154.5831 VDWAALS =
-1722.4791
EELEC = -18957.8588 EGB = -2739.4969 RESTRAINT =
4559.9479
EAMBER (non-restraint) = 1108.8572
------------------------------------------------------------------------------
NSTEP = 67 TIME(PS) = 0.217 TEMP(K) = 660.84 PRESS =
0.0
Etot = 13114.1485 EKtot = 7329.0650 EPtot =
5785.0834
BOND = 3718.7154 ANGLE = 4259.5401 DIHED =
3308.6668
1-4 NB = 1107.2907 1-4 EEL = 12156.7526 VDWAALS =
-1726.0994
EELEC = -18951.5276 EGB = -2742.3333 RESTRAINT =
4654.0782
EAMBER (non-restraint) = 1131.0053
------------------------------------------------------------------------------
NSTEP = 68 TIME(PS) = 0.218 TEMP(K) = 651.56 PRESS =
0.0
Etot = 13108.8742 EKtot = 7226.1319 EPtot =
5882.7423
BOND = 3728.8097 ANGLE = 4242.6393 DIHED =
3317.8207
1-4 NB = 1109.8133 1-4 EEL = 12156.5649 VDWAALS =
-1731.0582
EELEC = -18942.2871 EGB = -2744.4249 RESTRAINT =
4744.8645
EAMBER (non-restraint) = 1137.8778
------------------------------------------------------------------------------
NSTEP = 69 TIME(PS) = 0.219 TEMP(K) = 645.31 PRESS =
0.0
Etot = 13101.7366 EKtot = 7156.8678 EPtot =
5944.8688
BOND = 3746.1965 ANGLE = 4193.1466 DIHED =
3328.1020
1-4 NB = 1100.1963 1-4 EEL = 12155.5351 VDWAALS =
-1732.1109
EELEC = -18932.2502 EGB = -2746.0260 RESTRAINT =
4832.0794
EAMBER (non-restraint) = 1112.7894
------------------------------------------------------------------------------
NSTEP = 70 TIME(PS) = 0.220 TEMP(K) = 643.08 PRESS =
0.0
Etot = 13093.6154 EKtot = 7132.0658 EPtot =
5961.5495
BOND = 3760.6906 ANGLE = 4106.6332 DIHED =
3336.3595
1-4 NB = 1086.4642 1-4 EEL = 12154.9703 VDWAALS =
-1729.9062
EELEC = -18922.0990 EGB = -2747.3381 RESTRAINT =
4915.7750
EAMBER (non-restraint) = 1045.7746
------------------------------------------------------------------------------
NSTEP = 71 TIME(PS) = 0.221 TEMP(K) = 644.10 PRESS =
0.0
Etot = 13084.6631 EKtot = 7143.4559 EPtot =
5941.2072
BOND = 3765.4555 ANGLE = 3989.5834 DIHED =
3342.4904
1-4 NB = 1078.1097 1-4 EEL = 12154.7870 VDWAALS =
-1725.1685
EELEC = -18911.7755 EGB = -2748.4093 RESTRAINT =
4996.1345
EAMBER (non-restraint) = 945.0727
------------------------------------------------------------------------------
NSTEP = 72 TIME(PS) = 0.222 TEMP(K) = 646.84 PRESS =
0.0
Etot = 13075.2866 EKtot = 7173.7388 EPtot =
5901.5478
BOND = 3757.8471 ANGLE = 3861.3645 DIHED =
3346.3669
1-4 NB = 1077.1681 1-4 EEL = 12154.6285 VDWAALS =
-1718.5272
EELEC = -18901.3815 EGB = -2749.2902 RESTRAINT =
5073.3715
EAMBER (non-restraint) = 828.1763
------------------------------------------------------------------------------
NSTEP = 73 TIME(PS) = 0.223 TEMP(K) = 649.72 PRESS =
0.0
Etot = 13066.3761 EKtot = 7205.7059 EPtot =
5860.6702
BOND = 3739.9721 ANGLE = 3744.7194 DIHED =
3348.2490
1-4 NB = 1082.0220 1-4 EEL = 12154.6815 VDWAALS =
-1715.1521
EELEC = -18891.5520 EGB = -2749.9982 RESTRAINT =
5147.7284
EAMBER (non-restraint) = 712.9418
------------------------------------------------------------------------------
NSTEP = 74 TIME(PS) = 0.224 TEMP(K) = 651.37 PRESS =
0.0
Etot = 13056.5742 EKtot = 7224.0248 EPtot =
5832.5494
BOND = 3717.4352 ANGLE = 3657.2908 DIHED =
3348.5429
1-4 NB = 1087.7947 1-4 EEL = 12155.5166 VDWAALS =
-1719.7949
EELEC = -18883.0132 EGB = -2750.6672 RESTRAINT =
5219.4446
EAMBER (non-restraint) = 613.1048
------------------------------------------------------------------------------
NSTEP = 75 TIME(PS) = 0.225 TEMP(K) = 650.30 PRESS =
0.0
Etot = 13047.7650 EKtot = 7212.1754 EPtot =
5835.5896
BOND = 3696.1658 ANGLE = 3609.1546 DIHED =
3347.5255
1-4 NB = 1087.5547 1-4 EEL = 12157.3111 VDWAALS =
-1723.2715
EELEC = -18876.0185 EGB = -2751.5317 RESTRAINT =
5288.6997
EAMBER (non-restraint) = 546.8899
------------------------------------------------------------------------------
NSTEP = 76 TIME(PS) = 0.226 TEMP(K) = 645.24 PRESS =
0.0
Etot = 13039.8921 EKtot = 7156.0308 EPtot =
5883.8613
BOND = 3678.6535 ANGLE = 3602.1361 DIHED =
3345.0704
1-4 NB = 1088.3033 1-4 EEL = 12158.8873 VDWAALS =
-1721.5416
EELEC = -18870.3315 EGB = -2752.9030 RESTRAINT =
5355.5868
EAMBER (non-restraint) = 528.2746
------------------------------------------------------------------------------
NSTEP = 77 TIME(PS) = 0.227 TEMP(K) = 636.09 PRESS =
0.0
Etot = 13032.6558 EKtot = 7054.5936 EPtot =
5978.0621
BOND = 3662.2560 ANGLE = 3625.9128 DIHED =
3340.5663
1-4 NB = 1109.5608 1-4 EEL = 12159.2906 VDWAALS =
-1719.3620
EELEC = -18865.4322 EGB = -2754.8170 RESTRAINT =
5420.0868
EAMBER (non-restraint) = 557.9754
------------------------------------------------------------------------------
NSTEP = 78 TIME(PS) = 0.228 TEMP(K) = 630.19 PRESS =
0.0
Etot = 13047.3208 EKtot = 6989.1803 EPtot =
6058.1405
BOND = 3640.7912 ANGLE = 3651.4432 DIHED =
3334.4412
1-4 NB = 1151.0430 1-4 EEL = 12161.9155 VDWAALS =
-1745.3530
EELEC = -18860.9853 EGB = -2757.2182 RESTRAINT =
5482.0629
EAMBER (non-restraint) = 576.0776
------------------------------------------------------------------------------
NSTEP = 79 TIME(PS) = 0.229 TEMP(K) = 634.80 PRESS =
0.0
Etot = 13034.7181 EKtot = 7040.2600 EPtot =
5994.4581
BOND = 3607.9469 ANGLE = 3646.8071 DIHED =
3328.2379
1-4 NB = 1080.3209 1-4 EEL = 12174.1828 VDWAALS =
-1766.9309
EELEC = -18856.9374 EGB = -2760.4978 RESTRAINT =
5541.3285
EAMBER (non-restraint) = 453.1296
------------------------------------------------------------------------------
NSTEP = 80 TIME(PS) = 0.230 TEMP(K) = 633.82 PRESS =
0.0
Etot = 13029.7402 EKtot = 7029.3525 EPtot =
6000.3876
BOND = 3562.2907 ANGLE = 3653.1725 DIHED =
3318.1493
1-4 NB = 1076.6764 1-4 EEL = 12186.0978 VDWAALS =
-1775.5255
EELEC = -18854.0167 EGB = -2764.3065 RESTRAINT =
5597.8496
EAMBER (non-restraint) = 402.5380
------------------------------------------------------------------------------
NSTEP = 81 TIME(PS) = 0.231 TEMP(K) = 630.63 PRESS =
0.0
Etot = 13021.4634 EKtot = 6993.9839 EPtot =
6027.4795
BOND = 3506.6326 ANGLE = 3673.2341 DIHED =
3304.6002
1-4 NB = 1091.2518 1-4 EEL = 12197.3231 VDWAALS =
-1776.2053
EELEC = -18852.2722 EGB = -2768.7416 RESTRAINT =
5651.6567
EAMBER (non-restraint) = 375.8228
------------------------------------------------------------------------------
NSTEP = 82 TIME(PS) = 0.232 TEMP(K) = 625.82 PRESS =
0.0
Etot = 13012.8599 EKtot = 6940.6733 EPtot =
6072.1866
BOND = 3446.8360 ANGLE = 3704.0072 DIHED =
3290.4544
1-4 NB = 1116.8613 1-4 EEL = 12208.4408 VDWAALS =
-1772.0280
EELEC = -18851.4064 EGB = -2773.7682 RESTRAINT =
5702.7894
EAMBER (non-restraint) = 369.3972
------------------------------------------------------------------------------
NSTEP = 83 TIME(PS) = 0.233 TEMP(K) = 619.49 PRESS =
0.0
Etot = 13011.0580 EKtot = 6870.4366 EPtot =
6140.6213
BOND = 3390.0982 ANGLE = 3749.9910 DIHED =
3276.0574
1-4 NB = 1149.2352 1-4 EEL = 12219.7494 VDWAALS =
-1765.5807
EELEC = -18851.0644 EGB = -2779.0232 RESTRAINT =
5751.1586
EAMBER (non-restraint) = 389.4628
------------------------------------------------------------------------------
NSTEP = 84 TIME(PS) = 0.234 TEMP(K) = 615.62 PRESS =
0.0
Etot = 12999.4424 EKtot = 6827.5318 EPtot =
6171.9106
BOND = 3340.2476 ANGLE = 3798.3982 DIHED =
3262.1265
1-4 NB = 1137.9493 1-4 EEL = 12230.8989 VDWAALS =
-1759.0642
EELEC = -18851.0262 EGB = -2784.2793 RESTRAINT =
5796.6599
EAMBER (non-restraint) = 375.2507
------------------------------------------------------------------------------
NSTEP = 85 TIME(PS) = 0.235 TEMP(K) = 612.59 PRESS =
0.0
Etot = 12992.2531 EKtot = 6793.9340 EPtot =
6198.3191
BOND = 3297.9094 ANGLE = 3844.7735 DIHED =
3249.7131
1-4 NB = 1120.6009 1-4 EEL = 12241.2404 VDWAALS =
-1754.6195
EELEC = -18851.0594 EGB = -2789.5554 RESTRAINT =
5839.3163
EAMBER (non-restraint) = 359.0028
------------------------------------------------------------------------------
NSTEP = 86 TIME(PS) = 0.236 TEMP(K) = 607.28 PRESS =
0.0
Etot = 12982.5124 EKtot = 6735.0865 EPtot =
6247.4259
BOND = 3259.5472 ANGLE = 3882.4812 DIHED =
3240.5180
1-4 NB = 1134.3660 1-4 EEL = 12249.6045 VDWAALS =
-1753.0422
EELEC = -18850.7002 EGB = -2794.5327 RESTRAINT =
5879.1841
EAMBER (non-restraint) = 368.2418
------------------------------------------------------------------------------
vlimit exceeded for step 86; vmax = 44.5278
NSTEP = 87 TIME(PS) = 0.237 TEMP(K) = 605.22 PRESS =
0.0
Etot = 13240.7733 EKtot = 6712.1661 EPtot =
6528.6072
BOND = 3219.1993 ANGLE = 3899.2979 DIHED =
3234.7072
1-4 NB = 1403.0165 1-4 EEL = 12255.2141 VDWAALS =
-1750.5403
EELEC = -18849.5686 EGB = -2799.0631 RESTRAINT =
5916.3442
EAMBER (non-restraint) = 612.2630
------------------------------------------------------------------------------
vlimit exceeded for step 87; vmax = 22.6510
NSTEP = 88 TIME(PS) = 0.238 TEMP(K) = 663.75 PRESS =
0.0
Etot = 13531.7818 EKtot = 7361.3526 EPtot =
6170.4292
BOND = 3171.8068 ANGLE = 3837.0249 DIHED =
3231.3064
1-4 NB = 1116.0414 1-4 EEL = 12257.0050 VDWAALS =
-1743.2941
EELEC = -18847.1204 EGB = -2803.3878 RESTRAINT =
5951.0471
EAMBER (non-restraint) = 219.3821
------------------------------------------------------------------------------
vlimit exceeded for step 88; vmax = 21.2495
NSTEP = 89 TIME(PS) = 0.239 TEMP(K) = 660.57 PRESS =
0.0
Etot = 13478.3236 EKtot = 7326.0827 EPtot =
6152.2409
BOND = 3115.9329 ANGLE = 3840.3715 DIHED =
3229.3460
1-4 NB = 1109.7776 1-4 EEL = 12256.2677 VDWAALS =
-1733.6516
EELEC = -18843.5149 EGB = -2806.7089 RESTRAINT =
5984.4206
EAMBER (non-restraint) = 167.8203
------------------------------------------------------------------------------
vlimit exceeded for step 89; vmax = 23.6266
NSTEP = 90 TIME(PS) = 0.240 TEMP(K) = 650.95 PRESS =
0.0
Etot = 13425.9595 EKtot = 7219.3867 EPtot =
6206.5728
BOND = 3056.6908 ANGLE = 3907.4349 DIHED =
3227.9425
1-4 NB = 1114.4126 1-4 EEL = 12253.3039 VDWAALS =
-1723.3208
EELEC = -18838.6379 EGB = -2808.7714 RESTRAINT =
6017.5183
EAMBER (non-restraint) = 189.0545
------------------------------------------------------------------------------
A V E R A G E S O V E R 90 S T E P S
NSTEP = 90 TIME(PS) = 0.240 TEMP(K) = 583.89 PRESS =
0.0
Etot = 13313.7570 EKtot = 6475.6306 EPtot =
6838.1264
BOND = 7277.1610 ANGLE = 3813.8634 DIHED =
3181.0324
1-4 NB = 1155.7633 1-4 EEL = 12279.8904 VDWAALS =
-1756.1580
EELEC = -19116.1215 EGB = -2687.3690 RESTRAINT =
2690.0644
EAMBER (non-restraint) = 4148.0620
------------------------------------------------------------------------------
R M S F L U C T U A T I O N S
NSTEP = 90 TIME(PS) = 0.240 TEMP(K) = 165.79 PRESS =
0.0
Etot = 189.1246 EKtot = 1838.6757 EPtot =
1951.3681
BOND = 4221.9169 ANGLE = 444.0440 DIHED =
158.7642
1-4 NB = 51.2428 1-4 EEL = 128.3943 VDWAALS =
72.0712
EELEC = 205.1601 EGB = 60.8987 RESTRAINT =
2095.8154
EAMBER (non-restraint) = -144.4473
------------------------------------------------------------------------------
--------------------------------------------------------------------------------
5. TIMINGS
--------------------------------------------------------------------------------
| Calc gb radii 29.05 (19.02% of Gen B)
| Calc gb diag 54.24 (35.53% of Gen B)
| Calc gb off-diag 69.40 (45.45% of Gen B)
| Gen Born time 152.68 (100.0% of Nonbo)
| Nonbond force 152.68 (99.79% of Force)
| Bond/Angle/Dihedral 0.32 ( 0.21% of Force)
| Force time 153.01 (99.64% of Runmd)
| Shake time 0.02 ( 0.01% of Runmd)
| Verlet update time 0.54 ( 0.35% of Runmd)
| Runmd Time 153.57 (100.0% of Total)
| Other 0.08 ( 0.05% of Total)
| Total time 153.65 (100.0% of ALL )
| Highest rstack allocated: 0
| Highest istack allocated: 0
| Job began at 22:18:26.164 on 01/05/2002
| Setup done at 22:18:26.249 on 01/05/2002
| Run done at 22:20:59.815 on 01/05/2002
| wallclock() was called 2170 times
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
We can see that the results have problems from NSEEP=87. I want to know
the reason for this problem.
I also want to konw after finish the equilibration ,can I begin run TMD .
Besides that,I also have wonder aboutthe parallel command. I use the
following commmand ,however ,it can't run successfully: mpirun -np 4
$AMBERHOME/exe/sander.MPI ....................
I am looking for you replay and will be very grateful foryour kindhearted.
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Received on Tue Sep 11 2012 - 21:00:04 PDT
