Dear all
I do a MD simulation like the amber ionic liquid tutorial. for the first
step I do for 5ns. after the md finished the job was in the queue?
I copy the necessary file to another directory and restart MD, but the
simulation restarting from 3186 ps not from 5000 ps?
what could I do?
best regard
Nasiri
=============================================================
tail -100 md1.out
Ewald error estimate: 0.1647E-04
------------------------------------------------------------------------------
NSTEP = 4995000 TIME(PS) = 4995.000 TEMP(K) = 306.79 PRESS =
369.7
Etot = 110.7584 EKtot = 2064.8800 EPtot =
-1954.1216
BOND = 687.2929 ANGLE = 873.1544 DIHED =
169.9640
1-4 NB = 31.6772 1-4 EEL = 945.9037 VDWAALS =
-828.1005
EELEC = -3834.0133 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 266.4169 VIRIAL = 76.0272 VOLUME =
23853.2236
Density =
0.9624
Ewald error estimate: 0.6979E-06
------------------------------------------------------------------------------
NSTEP = 5000000 TIME(PS) = 5000.000 TEMP(K) = 300.06 PRESS =
-135.8
Etot = 22.0233 EKtot = 2019.5567 EPtot =
-1997.5333
BOND = 700.4772 ANGLE = 823.8397 DIHED =
173.2342
1-4 NB = 31.0197 1-4 EEL = 946.8374 VDWAALS =
-869.5587
EELEC = -3803.3828 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 300.1690 VIRIAL = 370.0495 VOLUME =
23840.3763
Density =
0.9629
Ewald error estimate: 0.2457E-03
------------------------------------------------------------------------------
A V E R A G E S O V E R 5000000 S T E P S
NSTEP = 5000000 TIME(PS) = 5000.000 TEMP(K) = 297.90 PRESS =
-3.4
Etot = 53.4122 EKtot = 2005.0617 EPtot =
-1951.6496
BOND = 698.9419 ANGLE = 869.5246 DIHED =
162.2404
1-4 NB = 31.4564 1-4 EEL = 944.0402 VDWAALS =
-847.0310
EELEC = -3810.8221 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 288.5973 VIRIAL = 291.9293 VOLUME =
24460.4248
Density =
0.9503
Ewald error estimate: 0.1498E-03
------------------------------------------------------------------------------
R M S F L U C T U A T I O N S
NSTEP = 5000000 TIME(PS) = 5000.000 TEMP(K) = 5.15 PRESS =
329.5
Etot = 77.0081 EKtot = 34.6406 EPtot =
68.4932
BOND = 22.4479 ANGLE = 20.9366 DIHED =
8.0117
1-4 NB = 2.1977 1-4 EEL = 2.3697 VDWAALS =
44.8811
EELEC = 39.7736 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 13.0234 VIRIAL = 172.7217 VOLUME =
3926.6309
Density =
0.0748
Ewald error estimate: 0.1136E-03
------------------------------------------------------------------------------
--------------------------------------------------------------------------------
5. TIMINGS
--------------------------------------------------------------------------------
| Build the list 9184.60 (98.77% of List )
| Other 114.18 ( 1.23% of List )
| List time 9298.78 ( 2.54% of Nonbo)
| Short_ene time 312434.00 (99.71% of Direc)
| Other 896.26 ( 0.29% of Direc)
| Direct Ewald time 313330.26 (87.85% of Ewald)
| Adjust Ewald time 2853.11 ( 0.80% of Ewald)
| Fill Bspline coeffs 1530.58 ( 3.85% of Recip)
| Fill charge grid 3737.07 ( 9.41% of Recip)
| Scalar sum 10494.56 (26.43% of Recip)
| Grad sum 5608.26 (14.12% of Recip)
| FFT time 18329.08 (46.16% of Recip)
| Other 9.62 ( 0.02% of Recip)
| Recip Ewald time 39709.17 (11.13% of Ewald)
| Force Adjust 31.91 ( 0.01% of Ewald)
| Virial junk 122.55 ( 0.03% of Ewald)
| Other 600.28 ( 0.17% of Ewald)
| Ewald time 356660.13 (97.46% of Nonbo)
| Nonbond force 365965.32 (99.01% of Force)
| Bond/Angle/Dihedral 3621.94 ( 0.98% of Force)
| Other 54.67 ( 0.01% of Force)
| Force time 369641.92 (98.08% of Runmd)
| Verlet update time 7083.53 ( 1.88% of Runmd)
| Ekcmr time 96.58 ( 0.03% of Runmd)
| Other 42.96 ( 0.01% of Runmd)
| Runmd Time 376865.00 (100.0% of Total)
| Total time 376865.15 (100.0% of ALL )
| Highest rstack allocated: 207308
| Highest istack allocated: 2258
| Final Performance Info:
| -----------------------------------------------------
| Average timings for all steps:
| Elapsed(s) = 376865.00 Per Step(ms) = 75.37
| ns/day = 1.15 seconds/ns = 75373.00
| -----------------------------------------------------
| Job began at 14:47:17.472 on 01/16/2014
| Setup done at 14:47:17.623 on 01/16/2014
| Run done at 23:28:22.624 on 01/20/2014
| wallclock() was called******** times
=============================================================
tail -200 md2.out
-------------------------------------------------------
Amber 12 SANDER 2012
-------------------------------------------------------
| PMEMD implementation of SANDER, Release 12
| Run on 01/20/2014 at 22:58:47
[-O]verwriting output
File Assignments:
| MDIN: mdin.in
| MDOUT:
md2.out
| INPCRD:
md1.x
| PARM:
ionicbox.prmtop
| RESTRT:
md2.x
| REFC:
refc
| MDVEL:
mdvel
| MDEN:
md2.dat
| MDCRD: md2.nc
| MDINFO:
mdinfo
Here is the input file:
equilibration for
box
&cntrl
imin=0, ntpr=5000,
ntwx=5000,
ntx=5,
irest=1,
tempi=298., temp0=298., ntt=3,
cut=12,
gamma_ln=5., ntb=2, ntp=1, taup=1.0, ioutfm=1,
nstlim=5000000,
ntwr=1000, dt=.001,
ig=-1,
&end
Note: ig = -1. Setting random seed based on wallclock time in microseconds.
| Conditional Compilation Defines Used:
| DIRFRC_COMTRANS
| DIRFRC_EFS
| DIRFRC_NOVEC
| PUBFFT
| FFTLOADBAL_2PROC
| BINTRAJ
| Largest sphere to fit in unit cell has radius = 14.297
| New format PARM file being parsed.
| Version = 1.000 Date = 01/01/14 Time = 16:48:05
| Note: 1-4 EEL scale factors are being read from the topology file.
| Note: 1-4 VDW scale factors are being read from the topology file.
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals
--------------------------------------------------------------------------------
1. RESOURCE USE:
--------------------------------------------------------------------------------
getting new box info from bottom of inpcrd
NATOM = 2258 NTYPES = 10 NBONH = 1454 MBONA = 501
NTHETH = 2693 MTHETA = 264 NPHIH = 1921 MPHIA = 374
NHPARM = 0 NPARM = 0 NNB = 7356 NRES = 325
NBONA = 501 NTHETA = 264 NPHIA = 374 NUMBND = 12
NUMANG = 21 NPTRA = 11 NATYP = 11 NPHB = 0
IFBOX = 1 NMXRS = 25 IFCAP = 0 NEXTRA = 0
NCOPY = 0
| Coordinate Index Table dimensions: 4 4 4
| Direct force subcell size = 7.1813 7.1813 7.1486
BOX TYPE: RECTILINEAR
--------------------------------------------------------------------------------
2. CONTROL DATA FOR THE RUN
--------------------------------------------------------------------------------
default_name
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 = 5000, ntrx = 1, ntwr =
1000
iwrap = 0, ntwx = 5000, ntwv = 0, ntwe
= 0
ioutfm = 1, ntwprt = 0, idecomp = 0,
rbornstat= 0
Potential function:
ntf = 1, ntb = 2, igb = 0, nsnb
= 25
ipol = 0, gbsa = 0, iesp = 0
dielc = 1.00000, cut = 12.00000, intdiel = 1.00000
Frozen or restrained atoms:
ibelly = 0, ntr = 0
Molecular dynamics:
nstlim = 5000000, nscm = 1000, nrespa = 1
t = 0.00000, dt = 0.00100, vlimit = 20.00000
Langevin dynamics temperature regulation:
ig = 986688
temp0 = 298.00000, tempi = 298.00000, gamma_ln= 5.00000
Pressure regulation:
ntp = 1
pres0 = 1.00000, comp = 44.60000, taup = 1.00000
| Intermolecular bonds treatment:
| no_intermolecular_bonds = 1
| Energy averages sample interval:
| ene_avg_sampling = 5000
Ewald parameters:
verbose = 0, ew_type = 0, nbflag = 1, use_pme
= 1
vdwmeth = 1, eedmeth = 1, netfrc = 1
Box X = 28.725 Box Y = 28.725 Box Z = 28.594
Alpha = 90.000 Beta = 90.000 Gamma = 90.000
NFFT1 = 30 NFFT2 = 30 NFFT3 = 30
Cutoff= 12.000 Tol =0.100E-04
Ewald Coefficient = 0.22664
Interpolation order = 4
--------------------------------------------------------------------------------
3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------
default_name
begin time read from input coords = 3181.000 ps
Number of triangulated 3-point waters found: 0
Sum of charges from parm topology file = -0.00004337
Forcing neutrality...
| Dynamic Memory, Types Used:
| Reals 233496
| Integers 120508
| Nonbonded Pairs Initial Allocation: 1122959
--------------------------------------------------------------------------------
4. RESULTS
--------------------------------------------------------------------------------
---------------------------------------------------
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 = 0.2738E-14 at 2.422500
| CHECK d/dx switch(x): max rel err = 0.7967E-11 at 2.716640
---------------------------------------------------
|---------------------------------------------------
| APPROXIMATING direct energy using CUBIC SPLINE INTERPOLATION
| with 50.0 points per unit in tabled values
| Relative Error Limit not exceeded for r .gt. 2.27
| APPROXIMATING direct force using CUBIC SPLINE INTERPOLATION
| with 50.0 points per unit in tabled values
| Relative Error Limit not exceeded for r .gt. 2.78
|---------------------------------------------------
NSTEP = 5000 TIME(PS) = 3186.000 TEMP(K) = 298.89 PRESS =
-383.5
Etot = 72.3120 EKtot = 2011.7339 EPtot =
-1939.4220
BOND = 684.8586 ANGLE = 887.5292 DIHED =
172.0031
1-4 NB = 29.7509 1-4 EEL = 947.8695 VDWAALS =
-881.9305
EELEC = -3779.5029 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 297.6092 VIRIAL = 493.6856 VOLUME =
23677.4832
Density =
0.9695
Ewald error estimate: 0.1282E-03
------------------------------------------------------------------------------
=============================================================
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Received on Mon Jan 20 2014 - 13:00:03 PST
