Dear Hannes,
I think I have a working protocol now, but I don’t understand the variation in pressure, the density is OK, is near 1 on equilibration and production which are NPT, but the pressure varies wildly, is that normal?
The ETOT is also stable, only I don’t understand teh variation in pressure… could you please tell me which units they are? And why it varias so wildly despite it should be NPT production as you can see in the example output below?
Thanks a lot again,
Fabian
-------------------------------------------------------
Amber 14 SANDER 2014
-------------------------------------------------------
| PMEMD implementation of SANDER, Release 14
| Run on 12/07/2015 at 16:31:58
| Executable path: /opt/amber14/bin/pmemd.MPI
| Working directory: /home/fabian/TUTORIALS/AMBER/A9/1HNN/prod1/0.1
| Hostname: amber.bi.technion.ac.il
[-O]verwriting output
File Assignments:
| MDIN: prod0.1.in
| MDOUT: prod0.1.out
| INPCRD: equil0.1.rst
| PARM: ../../prmtop/SKF_avo_solv.prmtop
| RESTRT: prod0.1.rst
| REFC: refc
| MDVEL: mdvel
| MDEN: prod0.1.en
| MDCRD: prod0.1.nc
| MDINFO: prod0.1.info
|LOGFILE: prod0.1.log
| MDFRC: mdfrc
Here is the input file:
Constant PRESSURE production 5ns
&cntrl
imin = 0,
nstlim = 2500000,
irest = 1,
ntx = 5,
dt = 0.002,
ntb=2,
ntp=1,
ntt=3,
taup = 2.0, pres0= 1.0,
gamma_ln=2.0
temp0 = 300.0,
ig = -1,
ntc = 2,
ntf = 1,
ntxo=2,
ioutfm = 1,
ntwe = 1000,
ntwx = 10000,
ntpr = 10000,
ntwr = 20000,
icfe = 1,
ifsc = 1,
clambda = 0.1,
scalpha = 0.5,
scbeta = 12.0,
logdvdl = 0,
ifmbar = 1,
bar_intervall = 100,
bar_l_min = 0.0,
bar_l_max = 1.0,
bar_l_incr = 0.1,
timask1='',
timask2=':1',
scmask1='',
scmask2=':1',
/
&ewald
/
Note: ig = -1. Setting random seed to 147324 based on wallclock time in
microseconds and disabling the synchronization of random numbers
between tasks to improve performance.
| Conditional Compilation Defines Used:
| MPI
| PUBFFT
| BINTRAJ
| EMIL
| Largest sphere to fit in unit cell has radius = 16.534
| New format PARM file being parsed.
| Version = 1.000 Date = 11/26/15 Time = 18:26:25
| 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 box info from netcdf restart file
NATOM = 5074 NTYPES = 12 NBONH = 5059 MBONA = 15
NTHETH = 29 MTHETA = 22 NPHIH = 52 MPHIA = 29
NHPARM = 0 NPARM = 0 NNB = 6882 NRES = 1684
NBONA = 15 NTHETA = 22 NPHIA = 29 NUMBND = 14
NUMANG = 23 NPTRA = 6 NATYP = 13 NPHB = 1
IFBOX = 2 NMXRS = 27 IFCAP = 0 NEXTRA = 0
NCOPY = 0
| Coordinate Index Table dimensions: 7 7 7
| Direct force subcell size = 5.7857 5.7857 5.7857
BOX TYPE: TRUNCATED OCTAHEDRON
--------------------------------------------------------------------------------
2. CONTROL DATA FOR THE RUN
--------------------------------------------------------------------------------
SKF
General flags:
imin = 0, nmropt = 0
Nature and format of input:
ntx = 5, irest = 1, ntrx = 1
Nature and format of output:
ntxo = 2, ntpr = 10000, ntrx = 1, ntwr = 20000
iwrap = 0, ntwx = 10000, ntwv = 0, ntwe = 1000
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 = 8.00000, intdiel = 1.00000
Frozen or restrained atoms:
ibelly = 0, ntr = 0
Molecular dynamics:
nstlim = 2500000, nscm = 1000, nrespa = 1
t = 0.00000, dt = 0.00200, vlimit = 20.00000
Langevin dynamics temperature regulation:
ig = 147324
temp0 = 300.00000, tempi = 0.00000, gamma_ln= 2.00000
Pressure regulation:
ntp = 1
pres0 = 1.00000, comp = 44.60000, taup = 2.00000
SHAKE:
ntc = 2, jfastw = 0
tol = 0.00001
Free energy options:
icfe = 1, ifsc = 1, klambda = 1
clambda = 0.1000, scalpha = 0.5000, scbeta = 12.0000
sceeorder = 2
dynlmb = 0.0000 logdvdl = 0
FEP MBAR options:
ifmbar = 1, bar_intervall = 100
bar_l_min =0.0000, bar_l_max =1.0000, bar_l_incr =0.1000
| Intermolecular bonds treatment:
| no_intermolecular_bonds = 1
| Energy averages sample interval:
| ene_avg_sampling = 10000
Ewald parameters:
verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1
vdwmeth = 1, eedmeth = 1, netfrc = 1
Box X = 40.500 Box Y = 40.500 Box Z = 40.500
Alpha = 109.471 Beta = 109.471 Gamma = 109.471
NFFT1 = 48 NFFT2 = 45 NFFT3 = 45
Cutoff= 8.000 Tol =0.100E-04
Ewald Coefficient = 0.34864
Interpolation order = 4
| PMEMD ewald parallel performance parameters:
| block_fft = 0
| fft_blk_y_divisor = 2
| excl_recip = 0
| excl_master = 0
| atm_redist_freq = 320
TI Mask 1 matches 0 atoms
TI Mask 2 :1; matches 27 atoms
TI region 1: 5047 atoms
TI region 2: 5074 atoms
SC Mask 2 :1; matches 27 atoms
MBAR - lambda values considered:
11 total: 0.0000 0.1000 0.2000 0.3000 0.4000 0.5000 0.6000 0.7000 0.8000 0.9000 1.0000
Extra energies will be computed 25000 times.
--------------------------------------------------------------------------------
3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------
SKF
begin time read from input coords = 75.000 ps
Molecule 1 is completely softcore and skipped for C.O.M..
Number of triangulated 3-point waters found: 1682
Number of shake restraints removed in TI region 1 : 0
Number of shake restraints removed in TI region 2 : 0
Sum of charges for TI region 1 = -1.00000000
Assuming uniform neutralizing plasma
Sum of charges for TI region 2 = 0.00100001
Forcing neutrality...
| Dynamic Memory, Types Used:
| Reals 473564
| Integers 310631
| Nonbonded Pairs Initial Allocation: 231374
| Running AMBER/MPI version on 5 nodes
--------------------------------------------------------------------------------
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 = 0.8332E-11 at 2.782960
---------------------------------------------------
|---------------------------------------------------
| APPROXIMATING direct energy using CUBIC SPLINE INTERPOLATION
| with 50.0 points per unit in tabled values
| Relative Error Limit not exceeded for r .gt. 2.47
| APPROXIMATING direct force using CUBIC SPLINE INTERPOLATION
| with 50.0 points per unit in tabled values
| Relative Error Limit not exceeded for r .gt. 2.89
|---------------------------------------------------
DOF for the SC part 2 of the system: 68
SHAKE constraints in the SC region: 13
MBAR Energy analysis:
Energy at 0.0000 = -16132.4501
Energy at 0.1000 = -16138.0128
Energy at 0.2000 = -16141.9638
Energy at 0.3000 = -16143.1561
Energy at 0.4000 = -16139.4432
Energy at 0.5000 = -16126.4643
Energy at 0.6000 = -16094.2788
Energy at 0.7000 = -16015.9804
Energy at 0.8000 = -15794.6150
Energy at 0.9000 = -14791.5721
Energy at 1.0000 = ************
------------------------------------------------------------------------------
| TI region 1
NSTEP = 10000 TIME(PS) = 95.000 TEMP(K) = 299.02 PRESS = -263.6
Etot = -13138.7621 EKtot = 2999.2506 EPtot = -16138.0128
BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000
1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 2341.4934
EELEC = -18479.5062 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 1507.6666 VIRIAL = 1799.4000 VOLUME = 51267.1407
Density = 0.9827
DV/DL = -48.9613
Ewald error estimate: 0.2369E-02
------------------------------------------------------------------------------
| TI region 2
NSTEP = 10000 TIME(PS) = 95.000 TEMP(K) = 299.22 PRESS = -263.6
Etot = -13116.5605 EKtot = 3021.4522 EPtot = -16138.0128
BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000
1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 2341.4934
EELEC = -18479.5062 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 1507.6666 VIRIAL = 1799.4000 VOLUME = 51267.1407
Density = 0.9896
DV/DL = -48.9613
Ewald error estimate: 0.2369E-02
------------------------------------------------------------------------------
Softcore part of the system: 27 atoms, TEMP(K) = 328.60
SC_Etot= -32.0568 SC_EKtot= 22.2016 SC_EPtot = -54.2584
SC_BOND= 9.0456 SC_ANGLE= 25.7206 SC_DIHED = 31.1407
SC_14NB= 5.9250 SC_14EEL= -159.6362 SC_VDW = -1.8101
SC_EEL = 35.3559
SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000
SC_EEL_DER= -2.1106 SC_VDW_DER= 8.7761 SC_DERIV = 6.6655
------------------------------------------------------------------------------
MBAR Energy analysis:
Energy at 0.0000 = -16120.8566
Energy at 0.1000 = -16124.6457
Energy at 0.2000 = -16125.6129
Energy at 0.3000 = -16121.7836
Energy at 0.4000 = -16109.4262
Energy at 0.5000 = -16080.8659
Energy at 0.6000 = -16018.3536
Energy at 0.7000 = -15873.0358
Energy at 0.8000 = -15465.6536
Energy at 0.9000 = -13601.9970
Energy at 1.0000 = ************
------------------------------------------------------------------------------
| TI region 1
NSTEP = 20000 TIME(PS) = 115.000 TEMP(K) = 296.48 PRESS = -73.1
Etot = -13150.8540 EKtot = 2973.7917 EPtot = -16124.6457
BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000
1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 2393.0278
EELEC = -18517.6734 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 1506.7929 VIRIAL = 1587.4762 VOLUME = 51143.6577
Density = 0.9850
DV/DL = -26.1668
Ewald error estimate: 0.2295E-02
------------------------------------------------------------------------------
| TI region 2
NSTEP = 20000 TIME(PS) = 115.000 TEMP(K) = 296.15 PRESS = -73.1
Etot = -13134.1692 EKtot = 2990.4765 EPtot = -16124.6457
BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000
1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 2393.0278
EELEC = -18517.6734 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 1506.7929 VIRIAL = 1587.4762 VOLUME = 51143.6577
Density = 0.9920
DV/DL = -26.1668
Ewald error estimate: 0.2295E-02
------------------------------------------------------------------------------
Softcore part of the system: 27 atoms, TEMP(K) = 246.95
SC_Etot= -32.1550 SC_EKtot= 16.6848 SC_EPtot = -48.8398
SC_BOND= 10.1670 SC_ANGLE= 29.5857 SC_DIHED = 30.7271
SC_14NB= 9.0010 SC_14EEL= -160.9910 SC_VDW = -1.8299
SC_EEL = 34.5003
SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000
SC_EEL_DER= -1.8727 SC_VDW_DER= 13.5965 SC_DERIV = 11.7238
------------------------------------------------------------------------------
MBAR Energy analysis:
Energy at 0.0000 = -16120.4724
Energy at 0.1000 = -16123.6372
Energy at 0.2000 = -16124.1710
Energy at 0.3000 = -16120.3402
Energy at 0.4000 = -16108.9231
Energy at 0.5000 = -16083.4129
Energy at 0.6000 = -16029.0538
Energy at 0.7000 = -15906.1245
Energy at 0.8000 = -15572.5241
Energy at 0.9000 = -14104.0963
Energy at 1.0000 = ************
------------------------------------------------------------------------------
| TI region 1
NSTEP = 30000 TIME(PS) = 135.000 TEMP(K) = 299.46 PRESS = 148.5
Etot = -13119.9637 EKtot = 3003.6734 EPtot = -16123.6372
BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000
1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 2422.2194
EELEC = -18545.8566 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 1505.8474 VIRIAL = 1341.7716 VOLUME = 51158.5930
Density = 0.9848
DV/DL = -20.6080
Ewald error estimate: 0.2186E-02
------------------------------------------------------------------------------
| TI region 2
NSTEP = 30000 TIME(PS) = 135.000 TEMP(K) = 300.04 PRESS = 148.5
Etot = -13093.8346 EKtot = 3029.8025 EPtot = -16123.6372
BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000
1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 2422.2194
EELEC = -18545.8566 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 1505.8474 VIRIAL = 1341.7716 VOLUME = 51158.5930
Density = 0.9917
DV/DL = -20.6080
Ewald error estimate: 0.2186E-02
------------------------------------------------------------------------------
Softcore part of the system: 27 atoms, TEMP(K) = 386.73
SC_Etot= -24.8633 SC_EKtot= 26.1291 SC_EPtot = -50.9924
SC_BOND= 7.4314 SC_ANGLE= 34.0650 SC_DIHED = 27.9506
SC_14NB= 6.9561 SC_14EEL= -161.4081 SC_VDW = -1.8131
SC_EEL = 35.8258
SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000
SC_EEL_DER= -0.5607 SC_VDW_DER= 11.5998 SC_DERIV = 11.0392
------------------------------------------------------------------------------
MBAR Energy analysis:
Energy at 0.0000 = -16137.9986
Energy at 0.1000 = -16140.1513
Energy at 0.2000 = -16139.5199
Energy at 0.3000 = -16134.2919
Energy at 0.4000 = -16121.1142
Energy at 0.5000 = -16093.2440
Energy at 0.6000 = -16035.4583
Energy at 0.7000 = -15906.9221
Energy at 0.8000 = -15561.6722
Energy at 0.9000 = -14043.6200
Energy at 1.0000 = ************
------------------------------------------------------------------------------
| TI region 1
NSTEP = 40000 TIME(PS) = 155.000 TEMP(K) = 300.48 PRESS = 213.7
Etot = -13126.2062 EKtot = 3013.9451 EPtot = -16140.1513
BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000
1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 2441.7467
EELEC = -18581.8980 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 1553.8509 VIRIAL = 1318.0131 VOLUME = 51104.8050
Density = 0.9858
DV/DL = -9.8221
Ewald error estimate: 0.1832E-02
------------------------------------------------------------------------------
| TI region 2
NSTEP = 40000 TIME(PS) = 155.000 TEMP(K) = 300.83 PRESS = 213.7
Etot = -13102.4256 EKtot = 3037.7258 EPtot = -16140.1513
BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000
1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 2441.7467
EELEC = -18581.8980 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 1553.8509 VIRIAL = 1318.0131 VOLUME = 51104.8050
Density = 0.9927
DV/DL = -9.8221
Ewald error estimate: 0.1832E-02
------------------------------------------------------------------------------
Softcore part of the system: 27 atoms, TEMP(K) = 351.97
SC_Etot= -24.8066 SC_EKtot= 23.7806 SC_EPtot = -48.5872
SC_BOND= 8.5164 SC_ANGLE= 27.1348 SC_DIHED = 30.9860
SC_14NB= 4.4614 SC_14EEL= -147.5209 SC_VDW = -1.6951
SC_EEL = 29.5302
SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000
SC_EEL_DER= -0.4727 SC_VDW_DER= 12.1775 SC_DERIV = 11.7047
------------------------------------------------------------------------------
MBAR Energy analysis:
Energy at 0.0000 = -16137.9470
Energy at 0.1000 = -16140.7608
Energy at 0.2000 = -16140.3234
Energy at 0.3000 = -16134.4034
Energy at 0.4000 = -16118.7861
Energy at 0.5000 = -16084.7875
Energy at 0.6000 = -16012.2177
Energy at 0.7000 = -15844.9329
Energy at 0.8000 = -15373.0781
Energy at 0.9000 = -13143.6807
Energy at 1.0000 = ************
------------------------------------------------------------------------------
| TI region 1
NSTEP = 50000 TIME(PS) = 175.000 TEMP(K) = 298.98 PRESS = 306.4
Etot = -13141.8626 EKtot = 2998.8982 EPtot = -16140.7608
BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000
1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 2495.7052
EELEC = -18636.4660 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 1512.5947 VIRIAL = 1173.1412 VOLUME = 51305.7869
Density = 0.9819
DV/DL = -14.5805
Ewald error estimate: 0.2121E-02
------------------------------------------------------------------------------
| TI region 2
NSTEP = 50000 TIME(PS) = 175.000 TEMP(K) = 298.72 PRESS = 306.4
Etot = -13124.2892 EKtot = 3016.4716 EPtot = -16140.7608
BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000
1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 2495.7052
EELEC = -18636.4660 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 1512.5947 VIRIAL = 1173.1412 VOLUME = 51305.7869
Density = 0.9888
DV/DL = -14.5805
Ewald error estimate: 0.2121E-02
------------------------------------------------------------------------------
Softcore part of the system: 27 atoms, TEMP(K) = 260.10
SC_Etot= -40.7441 SC_EKtot= 17.5734 SC_EPtot = -58.3175
SC_BOND= 8.1848 SC_ANGLE= 35.1642 SC_DIHED = 26.2121
SC_14NB= 8.4717 SC_14EEL= -168.5374 SC_VDW = -1.8928
SC_EEL = 34.0800
SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000
SC_EEL_DER= -1.5236 SC_VDW_DER= 15.0806 SC_DERIV = 13.5570
------------------------------------------------------------------------------
MBAR Energy analysis:
Energy at 0.0000 = -16137.7274
Energy at 0.1000 = -16143.5870
Energy at 0.2000 = -16147.6110
Energy at 0.3000 = -16148.5561
Energy at 0.4000 = -16144.1126
Energy at 0.5000 = -16129.6243
Energy at 0.6000 = -16094.5742
Energy at 0.7000 = -16010.8643
Energy at 0.8000 = -15779.5132
Energy at 0.9000 = -14782.1729
Energy at 1.0000 = 612130.4056
------------------------------------------------------------------------------
| TI region 1
NSTEP = 60000 TIME(PS) = 195.000 TEMP(K) = 294.00 PRESS = 22.7
Etot = -13194.7029 EKtot = 2948.8841 EPtot = -16143.5870
BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000
1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 2409.8474
EELEC = -18553.4344 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 1473.5777 VIRIAL = 1448.6301 VOLUME = 50895.0705
Density = 0.9899
DV/DL = -50.9339
Ewald error estimate: 0.2730E-02
------------------------------------------------------------------------------
| TI region 2
NSTEP = 60000 TIME(PS) = 195.000 TEMP(K) = 294.21 PRESS = 22.7
Etot = -13172.7134 EKtot = 2970.8736 EPtot = -16143.5870
BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000
1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 2409.8474
EELEC = -18553.4344 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 1473.5777 VIRIAL = 1448.6301 VOLUME = 50895.0705
Density = 0.9968
DV/DL = -50.9339
Ewald error estimate: 0.2730E-02
------------------------------------------------------------------------------
Softcore part of the system: 27 atoms, TEMP(K) = 325.46
SC_Etot= -19.4144 SC_EKtot= 21.9895 SC_EPtot = -41.4039
SC_BOND= 12.3341 SC_ANGLE= 44.5138 SC_DIHED = 28.5305
SC_14NB= 11.3819 SC_14EEL= -176.5835 SC_VDW = -1.7952
SC_EEL = 40.2145
SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000
SC_EEL_DER= -1.0547 SC_VDW_DER= 8.7169 SC_DERIV = 7.6622
------------------------------------------------------------------------------
MBAR Energy analysis:
Energy at 0.0000 = -16111.2384
Energy at 0.1000 = -16113.7358
Energy at 0.2000 = -16113.0058
Energy at 0.3000 = -16106.9396
Energy at 0.4000 = -16091.6290
Energy at 0.5000 = -16059.2116
Energy at 0.6000 = -15991.9714
Energy at 0.7000 = -15842.7227
Energy at 0.8000 = -15446.0260
Energy at 0.9000 = -13780.2921
Energy at 1.0000 = 5168342.8648
------------------------------------------------------------------------------
| TI region 1
NSTEP = 70000 TIME(PS) = 215.000 TEMP(K) = 302.69 PRESS = -194.9
Etot = -13077.6552 EKtot = 3036.0806 EPtot = -16113.7358
BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000
1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 2345.0756
EELEC = -18458.8113 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 1541.0781 VIRIAL = 1756.0288 VOLUME = 51081.8868
Density = 0.9862
DV/DL = -11.4125
Ewald error estimate: 0.2379E-02
------------------------------------------------------------------------------
| TI region 2
NSTEP = 70000 TIME(PS) = 215.000 TEMP(K) = 302.41 PRESS = -194.9
Etot = -13060.0145 EKtot = 3053.7213 EPtot = -16113.7358
BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000
1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 2345.0756
EELEC = -18458.8113 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 1541.0781 VIRIAL = 1756.0288 VOLUME = 51081.8868
Density = 0.9932
DV/DL = -11.4125
Ewald error estimate: 0.2379E-02
------------------------------------------------------------------------------
Softcore part of the system: 27 atoms, TEMP(K) = 261.09
SC_Etot= -30.1402 SC_EKtot= 17.6407 SC_EPtot = -47.7809
SC_BOND= 5.9670 SC_ANGLE= 29.6645 SC_DIHED = 28.1609
SC_14NB= 7.9046 SC_14EEL= -155.6791 SC_VDW = -1.8305
SC_EEL = 38.0316
SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000
SC_EEL_DER= -0.5357 SC_VDW_DER= 14.0966 SC_DERIV = 13.5609
------------------------------------------------------------------------------
MBAR Energy analysis:
Energy at 0.0000 = -16106.4518
Energy at 0.1000 = -16107.9213
Energy at 0.2000 = -16106.2736
Energy at 0.3000 = -16099.4702
Energy at 0.4000 = -16083.7122
Energy at 0.5000 = -16051.2838
Energy at 0.6000 = -15984.5205
Energy at 0.7000 = -15835.1050
Energy at 0.8000 = -15425.6023
Energy at 0.9000 = -13553.4044
Energy at 1.0000 = ************
------------------------------------------------------------------------------
| TI region 1
NSTEP = 80000 TIME(PS) = 235.000 TEMP(K) = 293.94 PRESS = 99.2
Etot = -13159.5707 EKtot = 2948.3506 EPtot = -16107.9213
BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000
1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 2420.1625
EELEC = -18528.0838 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 1481.8452 VIRIAL = 1371.9983 VOLUME = 51260.3437
Density = 0.9828
DV/DL = -1.5935
Ewald error estimate: 0.2098E-02
------------------------------------------------------------------------------
| TI region 2
NSTEP = 80000 TIME(PS) = 235.000 TEMP(K) = 293.71 PRESS = 99.2
Etot = -13142.0323 EKtot = 2965.8890 EPtot = -16107.9213
BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000
1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 2420.1625
EELEC = -18528.0838 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 1481.8452 VIRIAL = 1371.9983 VOLUME = 51260.3437
Density = 0.9897
DV/DL = -1.5935
Ewald error estimate: 0.2098E-02
------------------------------------------------------------------------------
Softcore part of the system: 27 atoms, TEMP(K) = 259.58
SC_Etot= -30.5707 SC_EKtot= 17.5384 SC_EPtot = -48.1091
SC_BOND= 3.8850 SC_ANGLE= 27.5699 SC_DIHED = 27.3102
SC_14NB= 6.4225 SC_14EEL= -149.2687 SC_VDW = -1.9470
SC_EEL = 37.9191
SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000
SC_EEL_DER= -0.2379 SC_VDW_DER= 13.3393 SC_DERIV = 13.1013
------------------------------------------------------------------------------
MBAR Energy analysis:
Energy at 0.0000 = -16201.9492
Energy at 0.1000 = -16204.0874
Energy at 0.2000 = -16203.8123
Energy at 0.3000 = -16199.4751
Energy at 0.4000 = -16187.9775
Energy at 0.5000 = -16162.9729
Energy at 0.6000 = -16109.8105
Energy at 0.7000 = -15988.0962
Energy at 0.8000 = -15648.5089
Energy at 0.9000 = -14077.2085
Energy at 1.0000 = ************
------------------------------------------------------------------------------
| TI region 1
NSTEP = 90000 TIME(PS) = 255.000 TEMP(K) = 300.73 PRESS = -52.0
Etot = -13187.7007 EKtot = 3016.3867 EPtot = -16204.0874
BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000
1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 2427.7629
EELEC = -18631.8503 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 1520.2029 VIRIAL = 1577.5922 VOLUME = 51096.3969
Density = 0.9860
DV/DL = -11.3146
Ewald error estimate: 0.1272E-02
------------------------------------------------------------------------------
| TI region 2
NSTEP = 90000 TIME(PS) = 255.000 TEMP(K) = 300.48 PRESS = -52.0
Etot = -13169.8792 EKtot = 3034.2082 EPtot = -16204.0874
BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000
1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 2427.7629
EELEC = -18631.8503 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 1520.2029 VIRIAL = 1577.5922 VOLUME = 51096.3969
Density = 0.9929
DV/DL = -11.3146
Ewald error estimate: 0.1272E-02
------------------------------------------------------------------------------
Softcore part of the system: 27 atoms, TEMP(K) = 263.77
SC_Etot= -42.9423 SC_EKtot= 17.8215 SC_EPtot = -60.7639
SC_BOND= 12.3567 SC_ANGLE= 25.2836 SC_DIHED = 33.3480
SC_14NB= 7.4679 SC_14EEL= -155.4844 SC_VDW = -1.7709
SC_EEL = 18.0353
SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000
SC_EEL_DER= -1.2785 SC_VDW_DER= 11.3455 SC_DERIV = 10.0669
------------------------------------------------------------------------------
MBAR Energy analysis:
Energy at 0.0000 = -16143.9965
Energy at 0.1000 = -16148.8951
Energy at 0.2000 = -16151.4530
Energy at 0.3000 = -16149.9808
Energy at 0.4000 = -16141.2602
Energy at 0.5000 = -16118.6106
Energy at 0.6000 = -16066.3996
Energy at 0.7000 = -15940.9418
Energy at 0.8000 = -15578.5595
Energy at 0.9000 = -13848.1051
Energy at 1.0000 = ************
------------------------------------------------------------------------------
| TI region 1
NSTEP = 100000 TIME(PS) = 275.000 TEMP(K) = 295.37 PRESS = 134.5
Etot = -13186.2145 EKtot = 2962.6806 EPtot = -16148.8951
BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000
1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 2438.8623
EELEC = -18587.7575 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 1502.4018 VIRIAL = 1353.8527 VOLUME = 51159.7606
Density = 0.9847
DV/DL = -39.3153
Ewald error estimate: 0.2416E-02
------------------------------------------------------------------------------
| TI region 2
NSTEP = 100000 TIME(PS) = 275.000 TEMP(K) = 295.34 PRESS = 134.5
Etot = -13166.5628 EKtot = 2982.3324 EPtot = -16148.8951
BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000
1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 2438.8623
EELEC = -18587.7575 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 1502.4018 VIRIAL = 1353.8527 VOLUME = 51159.7606
Density = 0.9917
DV/DL = -39.3153
Ewald error estimate: 0.2416E-02
------------------------------------------------------------------------------
Softcore part of the system: 27 atoms, TEMP(K) = 290.86
SC_Etot= -34.7595 SC_EKtot= 19.6517 SC_EPtot = -54.4112
SC_BOND= 5.4155 SC_ANGLE= 37.9892 SC_DIHED = 27.3860
SC_14NB= 8.2652 SC_14EEL= -164.9373 SC_VDW = -0.8279
SC_EEL = 32.2981
SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000
SC_EEL_DER= -2.2978 SC_VDW_DER= 11.9684 SC_DERIV = 9.6706
------------------------------------------------------------------------------
MBAR Energy analysis:
Energy at 0.0000 = -16122.9067
Energy at 0.1000 = -16126.5694
Energy at 0.2000 = -16128.1965
Energy at 0.3000 = -16126.3489
Energy at 0.4000 = -16118.2997
Energy at 0.5000 = -16098.4225
Energy at 0.6000 = -16053.6453
Energy at 0.7000 = -15947.7588
Energy at 0.8000 = -15646.6024
Energy at 0.9000 = -14236.3571
Energy at 1.0000 = ************
------------------------------------------------------------------------------
| TI region 1
NSTEP = 110000 TIME(PS) = 295.000 TEMP(K) = 295.60 PRESS = -205.7
Etot = -13161.5839 EKtot = 2964.9854 EPtot = -16126.5694
BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000
1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 2359.4684
EELEC = -18486.0377 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 1488.4259 VIRIAL = 1715.3828 VOLUME = 51111.4021
Density = 0.9857
DV/DL = -28.1857
Ewald error estimate: 0.2396E-02
------------------------------------------------------------------------------
| TI region 2
NSTEP = 110000 TIME(PS) = 295.000 TEMP(K) = 295.50 PRESS = -205.7
Etot = -13142.6315 EKtot = 2983.9379 EPtot = -16126.5694
BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000
1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 2359.4684
EELEC = -18486.0377 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 1488.4259 VIRIAL = 1715.3828 VOLUME = 51111.4021
Density = 0.9926
DV/DL = -28.1857
Ewald error estimate: 0.2396E-02
------------------------------------------------------------------------------
Softcore part of the system: 27 atoms, TEMP(K) = 280.51
SC_Etot= -33.3644 SC_EKtot= 18.9524 SC_EPtot = -52.3168
SC_BOND= 9.9485 SC_ANGLE= 31.2120 SC_DIHED = 29.3771
SC_14NB= 7.5128 SC_14EEL= -162.8664 SC_VDW = -1.7712
SC_EEL = 34.2704
SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000
SC_EEL_DER= -1.6772 SC_VDW_DER= 10.1180 SC_DERIV = 8.4408
------------------------------------------------------------------------------
MBAR Energy analysis:
Energy at 0.0000 = -16186.4692
Energy at 0.1000 = -16190.6044
Energy at 0.2000 = -16192.1712
Energy at 0.3000 = -16189.3305
Energy at 0.4000 = -16178.5932
Energy at 0.5000 = -16152.7526
Energy at 0.6000 = -16095.0494
Energy at 0.7000 = -15959.0217
Energy at 0.8000 = -15572.5151
Energy at 0.9000 = -13771.8704
Energy at 1.0000 = ************
------------------------------------------------------------------------------
| TI region 1
NSTEP = 120000 TIME(PS) = 315.000 TEMP(K) = 298.80 PRESS = 215.6
Etot = -13193.5580 EKtot = 2997.0464 EPtot = -16190.6044
BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000
1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 2469.3180
EELEC = -18659.9224 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 1518.5026 VIRIAL = 1281.1518 VOLUME = 50993.0632
Density = 0.9880
DV/DL = -30.7272
Ewald error estimate: 0.2243E-02
------------------------------------------------------------------------------
| TI region 2
NSTEP = 120000 TIME(PS) = 315.000 TEMP(K) = 298.90 PRESS = 215.6
Etot = -13172.3558 EKtot = 3018.2486 EPtot = -16190.6044
BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000
1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 2469.3180
EELEC = -18659.9224 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 1518.5026 VIRIAL = 1281.1518 VOLUME = 50993.0632
Density = 0.9949
DV/DL = -30.7272
Ewald error estimate: 0.2243E-02
------------------------------------------------------------------------------
Softcore part of the system: 27 atoms, TEMP(K) = 313.81
SC_Etot= -31.7686 SC_EKtot= 21.2022 SC_EPtot = -52.9708
SC_BOND= 6.7132 SC_ANGLE= 37.0077 SC_DIHED = 32.0599
SC_14NB= 7.0915 SC_14EEL= -164.8713 SC_VDW = -1.8569
SC_EEL = 30.8850
SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000
SC_EEL_DER= -2.4616 SC_VDW_DER= 13.0859 SC_DERIV = 10.6244
------------------------------------------------------------------------------
MBAR Energy analysis:
Energy at 0.0000 = -16075.6215
Energy at 0.1000 = -16080.7438
Energy at 0.2000 = -16084.2101
Energy at 0.3000 = -16084.8248
Energy at 0.4000 = -16080.3275
Energy at 0.5000 = -16066.0758
Energy at 0.6000 = -16031.3601
Energy at 0.7000 = -15946.8448
Energy at 0.8000 = -15706.0371
Energy at 0.9000 = -14622.7101
Energy at 1.0000 = ************
------------------------------------------------------------------------------
| TI region 1
NSTEP = 130000 TIME(PS) = 335.000 TEMP(K) = 302.18 PRESS = -166.8
Etot = -13049.7629 EKtot = 3030.9809 EPtot = -16080.7438
BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000
1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 2367.4805
EELEC = -18448.2243 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 1511.3371 VIRIAL = 1696.2747 VOLUME = 51351.9386
Density = 0.9811
DV/DL = -44.3871
Ewald error estimate: 0.2363E-02
------------------------------------------------------------------------------
Dr. Fabian Glaser
Head of the Structural Bioinformatics section
Bioinformatics Knowledge Unit - BKU
The Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering
Technion - Israel Institute of Technology, Haifa 32000, ISRAEL
fglaser at technion dot ac dot il
Tel: +972 4 8293701
http://bku.technion.ac.il
> On 4 Dec 2015, at 4:21 PM, Hannes Loeffler <Hannes.Loeffler.stfc.ac.uk> wrote:
>
> On Fri, 4 Dec 2015 14:09:29 +0200
> Fabian Glaser <fabian.glaser.gmail.com> wrote:
>
>> Thanks a lot!
>>
>> So no registration?
>
> What is registration?
>
>
>> Just min then heating at constant pressure and
>> then production at constantvpressure will do it for every lambda? No
>> volume equilibration necessary?
>
> Heating would occur at constant volume. Constant pressure will adjust
> the volume.
>
>
>> Finally what about your preferred tool for the final analysis for DG
>> of hydration? I know there are several.
>
> I use https://github.com/MobleyLab/alchemical-analysis . I am writing
> the AMBER parser for this tool. My code is not merged in yet but I hope
> this to happen today, otherwise:
> https://github.com/halx/alchemical-analysis for the fork of mine.
>
>
> Cheers,
> Hannes.
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Mon Dec 07 2015 - 07:00:04 PST
