Hi All, I
I am getting familiar with amber GPU MD. I was running GPU benchmark
calculations using input files from ambermd.org/gups
(cellulose_production_NPT).
My system details are:
Processor: Intel(R) Core(TM) i7-4820K CPU . 3.70GHz
Cuda : VIDIA-SMI 331.62 Driver Version: 331.62
Graphics card : GeForce GTX 770, 2GB
ASUS P9X79 Motherboard
The input file for running MD is
Typical Production MD NVT
&cntrl
ntx=5, irest=1,
ntc=2, ntf=2,
nstlim=10000,
ntpr=1000, ntwx=1000,
ntwr=10000,
dt=0.002, cut=8.,
ntt=1, tautp=10.0,
temp0=300.0,
ntb=2, ntp=1, barostat=2,
ioutfm=1,
/
I have few queries
1) In this input file, do we have to specify ntb=2? if we have barostat=2.
2) Anyway when I ran this calculations, using topology and coordinate files
provided, I got the error in the input file, which is pasted at the end of
message. In short I am getting this error, which I don't understand. It
seems odd!
Any suggestions will be helpful.
Regards,
Raman
Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| MC Barostat: Decreasing size of volume moves
check COM velocity, temp: 0.000589 0.00(Removed)
Here is complete output file:
-------------------------------------------------------
Amber 14 SANDER 2014
-------------------------------------------------------
| PMEMD implementation of SANDER, Release 14
| Run on 07/24/2014 at 19:06:21
| Executable path: /home/rparkesh/Documents/amber14/bin/pmemd.cuda
| Working directory:
/home/rparkesh/Desktop/Amber14_GPU_Benchmark_Suite/Amber14_Benchmark_Suite/PME/Cellulose_production_NPT
| Hostname: Unknown
[-O]verwriting output
File Assignments:
| MDIN:
mdin.GPU
| MDOUT:
mdin_gpu.out
| INPCRD:
inpcrd
| PARM:
prmtop
| RESTRT:
mdin_gpu.rst
| REFC:
refc
| MDVEL:
mdvel
| MDEN:
mden
| MDCRD:
mdin_gpu.mdcrd
| MDINFO:
mdinfo
| MDFRC:
mdfrc
Here is the input file:
Typical Production MD
NVT
&cntrl
ntx=5,
irest=1,
ntc=2,
ntf=2,
nstlim=10000,
ntpr=1000,
ntwx=1000,
ntwr=10000,
dt=0.002,
cut=8.,
ntt=1,
tautp=10.0,
temp0=300.0,
ntb=2, ntp=1,
barostat=2,
ioutfm=1,
/
|--------------------- INFORMATION ----------------------
| GPU (CUDA) Version of PMEMD in use: NVIDIA GPU IN USE.
| Version 14.0
|
| 01/31/2014
|
| Implementation by:
| Ross C. Walker (SDSC)
| Scott Le Grand (nVIDIA)
|
| CAUTION: The CUDA code is currently experimental.
| You use it at your own risk. Be sure to
| check ALL results carefully.
|
| Precision model in use:
| [SPFP] - Mixed Single/Double/Fixed Point Precision.
| (Default)
|
|--------------------------------------------------------
|----------------- CITATION INFORMATION -----------------
|
| When publishing work that utilized the CUDA version
| of AMBER, please cite the following in addition to
| the regular AMBER citations:
|
| - Romelia Salomon-Ferrer; Andreas W. Goetz; Duncan
| Poole; Scott Le Grand; Ross C. Walker "Routine
| microsecond molecular dynamics simulations with
| AMBER - Part II: Particle Mesh Ewald", J. Chem.
| Theory Comput., 2013, 9 (9), pp3878-3888,
| DOI: 10.1021/ct400314y.
|
| - Andreas W. Goetz; Mark J. Williamson; Dong Xu;
| Duncan Poole; Scott Le Grand; Ross C. Walker
| "Routine microsecond molecular dynamics simulations
| with AMBER - Part I: Generalized Born", J. Chem.
| Theory Comput., 2012, 8 (5), pp1542-1555.
|
| - Scott Le Grand; Andreas W. Goetz; Ross C. Walker
| "SPFP: Speed without compromise - a mixed precision
| model for GPU accelerated molecular dynamics
| simulations.", Comp. Phys. Comm., 2013, 184
| pp374-380, DOI: 10.1016/j.cpc.2012.09.022
|
|--------------------------------------------------------
|------------------- GPU DEVICE INFO --------------------
|
| CUDA_VISIBLE_DEVICES: not set
| CUDA Capable Devices Detected: 1
| CUDA Device ID in use: 0
| CUDA Device Name: GeForce GTX 770
| CUDA Device Global Mem Size: 2047 MB
| CUDA Device Num Multiprocessors: 8
| CUDA Device Core Freq: 1.08 GHz
|
|--------------------------------------------------------
| Conditional Compilation Defines Used:
| PUBFFT
| BINTRAJ
| CUDA
| EMIL
| Largest sphere to fit in unit cell has radius = 61.751
| New format PARM file being parsed.
| Version = 1.000 Date = 05/13/05 Time = 14:32:09
| Note: 1-4 EEL scale factors were NOT found in the topology file.
| Using default value of 1.2.
| Note: 1-4 VDW scale factors were NOT found in the topology file.
| Using default value of 2.0.
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals
--------------------------------------------------------------------------------
1. RESOURCE USE:
--------------------------------------------------------------------------------
getting new box info from bottom of inpcrd
NATOM = 408609 NTYPES = 8 NBONH = 360981 MBONA = 51840
NTHETH = 99576 MTHETA = 77652 NPHIH = 181764 MPHIA = 155196
NHPARM = 0 NPARM = 0 NNB = 976704 NRES = 110283
NBONA = 51840 NTHETA = 77652 NPHIA = 155196 NUMBND = 8
NUMANG = 14 NPTRA = 18 NATYP = 8 NPHB = 1
IFBOX = 1 NMXRS = 22 IFCAP = 0 NEXTRA = 0
NCOPY = 0
| Coordinate Index Table dimensions: 57 27 27
| Direct force subcell size = 4.5479 4.6133 4.5742
BOX TYPE: RECTILINEAR
--------------------------------------------------------------------------------
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 = 1000, ntrx = 1, ntwr =
10000
iwrap = 0, ntwx = 1000, ntwv = 0, ntwe
= 0
ioutfm = 1, ntwprt = 0, idecomp = 0,
rbornstat= 0
Potential function:
ntf = 2, 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 = 10000, nscm = 1000, nrespa = 1
t = 0.00000, dt = 0.00200, vlimit = -1.00000
Berendsen (weak-coupling) temperature regulation:
temp0 = 300.00000, tempi = 0.00000, tautp = 10.00000
Pressure regulation:
ntp = 1
pres0 = 1.00000, comp = 44.60000, taup = 1.00000
Monte-Carlo Barostat:
mcbarint = 100
SHAKE:
ntc = 2, jfastw = 0
tol = 0.00001
| Intermolecular bonds treatment:
| no_intermolecular_bonds = 1
| Energy averages sample interval:
| ene_avg_sampling = 1000
Ewald parameters:
verbose = 0, ew_type = 0, nbflag = 1, use_pme
= 1
vdwmeth = 1, eedmeth = 1, netfrc = 1
Box X = 259.230 Box Y = 124.558 Box Z = 123.502
Alpha = 90.000 Beta = 90.000 Gamma = 90.000
NFFT1 = 256 NFFT2 = 128 NFFT3 = 128
Cutoff= 8.000 Tol =0.100E-04
Ewald Coefficient = 0.34864
Interpolation order = 4
--------------------------------------------------------------------------------
3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------
begin time read from input coords = 20.020 ps
Number of triangulated 3-point waters found: 105855
Sum of charges from parm topology file = 0.00000000
Forcing neutrality...
| Dynamic Memory, Types Used:
| Reals 15649305
| Integers 18277903
| Nonbonded Pairs Initial Allocation: 68247918
| GPU memory information (estimate):
| KB of GPU memory in use: 895638
| KB of CPU memory in use: 448464
--------------------------------------------------------------------------------
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
|---------------------------------------------------
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| MC Barostat: Decreasing size of volume moves
check COM velocity, temp: 0.000589 0.00(Removed)
NSTEP = 1000 TIME(PS) = 22.020 TEMP(K) = 300.40 PRESS =
0.0
Etot = -443245.2458 EKtot = 258135.2031 EPtot =
-701380.4489
BOND = 20679.5493 ANGLE = 54023.0417 DIHED =
23639.6058
1-4 NB = 21691.1816 1-4 EEL = 742069.3050 VDWAALS =
96766.7985
EELEC = -1660249.9308 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME =
3987782.5027
Density =
1.0866
------------------------------------------------------------------------------
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| MC Barostat: Decreasing size of volume moves
check COM velocity, temp: 0.000008 0.00(Removed)
NSTEP = 2000 TIME(PS) = 24.020 TEMP(K) = 299.19 PRESS =
0.0
Etot = -443235.5829 EKtot = 257098.3594 EPtot =
-700333.9423
BOND = 20565.2372 ANGLE = 54204.1891 DIHED =
23594.0464
1-4 NB = 21706.4872 1-4 EEL = 741830.2738 VDWAALS =
97102.2262
EELEC = -1659336.4022 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME =
3987782.5027
Density =
1.0866
------------------------------------------------------------------------------
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| MC Barostat: Decreasing size of volume moves
check COM velocity, temp: 0.000013 0.00(Removed)
NSTEP = 3000 TIME(PS) = 26.020 TEMP(K) = 299.88 PRESS =
0.0
Etot = -443239.1740 EKtot = 257684.0000 EPtot =
-700923.1740
BOND = 20388.4613 ANGLE = 54052.9190 DIHED =
23593.7124
1-4 NB = 21723.3563 1-4 EEL = 741912.6123 VDWAALS =
97405.1247
EELEC = -1659999.3600 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME =
3987782.5027
Density =
1.0866
------------------------------------------------------------------------------
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Succeeded
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Succeeded
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| MC Barostat: Decreasing size of volume moves
check COM velocity, temp: 0.000016 0.00(Removed)
NSTEP = 4000 TIME(PS) = 28.020 TEMP(K) = 300.72 PRESS =
0.0
Etot = -443251.6570 EKtot = 258409.7969 EPtot =
-701661.4538
BOND = 20402.5563 ANGLE = 53916.7519 DIHED =
23587.6098
1-4 NB = 21732.2500 1-4 EEL = 742120.1837 VDWAALS =
96905.9092
EELEC = -1660326.7147 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME =
3986435.1378
Density =
1.0870
------------------------------------------------------------------------------
-------------------------------------------------------
Amber 14 SANDER 2014
-------------------------------------------------------
| PMEMD implementation of SANDER, Release 14
| Run on 07/24/2014 at 19:06:21
| Executable path: /home/rparkesh/Documents/amber14/bin/pmemd.cuda
| Working directory:
/home/rparkesh/Desktop/Amber14_GPU_Benchmark_Suite/Amber14_Benchmark_Suite/PME/Cellulose_production_NPT
| Hostname: Unknown
[-O]verwriting output
File Assignments:
| MDIN:
mdin.GPU
| MDOUT:
mdin_gpu.out
| INPCRD:
inpcrd
| PARM:
prmtop
| RESTRT:
mdin_gpu.rst
| REFC:
refc
| MDVEL:
mdvel
| MDEN:
mden
| MDCRD:
mdin_gpu.mdcrd
| MDINFO:
mdinfo
| MDFRC:
mdfrc
Here is the input file:
Typical Production MD
NVT
&cntrl
ntx=5,
irest=1,
ntc=2,
ntf=2,
nstlim=10000,
ntpr=1000,
ntwx=1000,
ntwr=10000,
dt=0.002,
cut=8.,
ntt=1,
tautp=10.0,
temp0=300.0,
ntb=2, ntp=1,
barostat=2,
ioutfm=1,
/
|--------------------- INFORMATION ----------------------
| GPU (CUDA) Version of PMEMD in use: NVIDIA GPU IN USE.
| Version 14.0
|
| 01/31/2014
|
| Implementation by:
| Ross C. Walker (SDSC)
| Scott Le Grand (nVIDIA)
|
| CAUTION: The CUDA code is currently experimental.
| You use it at your own risk. Be sure to
| check ALL results carefully.
|
| Precision model in use:
| [SPFP] - Mixed Single/Double/Fixed Point Precision.
| (Default)
|
|--------------------------------------------------------
|----------------- CITATION INFORMATION -----------------
|
| When publishing work that utilized the CUDA version
| of AMBER, please cite the following in addition to
| the regular AMBER citations:
|
| - Romelia Salomon-Ferrer; Andreas W. Goetz; Duncan
| Poole; Scott Le Grand; Ross C. Walker "Routine
| microsecond molecular dynamics simulations with
| AMBER - Part II: Particle Mesh Ewald", J. Chem.
| Theory Comput., 2013, 9 (9), pp3878-3888,
| DOI: 10.1021/ct400314y.
|
| - Andreas W. Goetz; Mark J. Williamson; Dong Xu;
| Duncan Poole; Scott Le Grand; Ross C. Walker
| "Routine microsecond molecular dynamics simulations
| with AMBER - Part I: Generalized Born", J. Chem.
| Theory Comput., 2012, 8 (5), pp1542-1555.
|
| - Scott Le Grand; Andreas W. Goetz; Ross C. Walker
| "SPFP: Speed without compromise - a mixed precision
| model for GPU accelerated molecular dynamics
| simulations.", Comp. Phys. Comm., 2013, 184
| pp374-380, DOI: 10.1016/j.cpc.2012.09.022
|
|--------------------------------------------------------
|------------------- GPU DEVICE INFO --------------------
|
| CUDA_VISIBLE_DEVICES: not set
| CUDA Capable Devices Detected: 1
| CUDA Device ID in use: 0
| CUDA Device Name: GeForce GTX 770
| CUDA Device Global Mem Size: 2047 MB
| CUDA Device Num Multiprocessors: 8
| CUDA Device Core Freq: 1.08 GHz
|
|--------------------------------------------------------
| Conditional Compilation Defines Used:
| PUBFFT
| BINTRAJ
| CUDA
| EMIL
| Largest sphere to fit in unit cell has radius = 61.751
| New format PARM file being parsed.
| Version = 1.000 Date = 05/13/05 Time = 14:32:09
| Note: 1-4 EEL scale factors were NOT found in the topology file.
| Using default value of 1.2.
| Note: 1-4 VDW scale factors were NOT found in the topology file.
| Using default value of 2.0.
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals
--------------------------------------------------------------------------------
1. RESOURCE USE:
--------------------------------------------------------------------------------
getting new box info from bottom of inpcrd
NATOM = 408609 NTYPES = 8 NBONH = 360981 MBONA = 51840
NTHETH = 99576 MTHETA = 77652 NPHIH = 181764 MPHIA = 155196
NHPARM = 0 NPARM = 0 NNB = 976704 NRES = 110283
NBONA = 51840 NTHETA = 77652 NPHIA = 155196 NUMBND = 8
NUMANG = 14 NPTRA = 18 NATYP = 8 NPHB = 1
IFBOX = 1 NMXRS = 22 IFCAP = 0 NEXTRA = 0
NCOPY = 0
| Coordinate Index Table dimensions: 57 27 27
| Direct force subcell size = 4.5479 4.6133 4.5742
BOX TYPE: RECTILINEAR
--------------------------------------------------------------------------------
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 = 1000, ntrx = 1, ntwr =
10000
iwrap = 0, ntwx = 1000, ntwv = 0, ntwe
= 0
ioutfm = 1, ntwprt = 0, idecomp = 0,
rbornstat= 0
Potential function:
ntf = 2, 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 = 10000, nscm = 1000, nrespa = 1
t = 0.00000, dt = 0.00200, vlimit = -1.00000
Berendsen (weak-coupling) temperature regulation:
temp0 = 300.00000, tempi = 0.00000, tautp = 10.00000
Pressure regulation:
ntp = 1
pres0 = 1.00000, comp = 44.60000, taup = 1.00000
Monte-Carlo Barostat:
mcbarint = 100
SHAKE:
ntc = 2, jfastw = 0
tol = 0.00001
| Intermolecular bonds treatment:
| no_intermolecular_bonds = 1
| Energy averages sample interval:
| ene_avg_sampling = 1000
Ewald parameters:
verbose = 0, ew_type = 0, nbflag = 1, use_pme
= 1
vdwmeth = 1, eedmeth = 1, netfrc = 1
Box X = 259.230 Box Y = 124.558 Box Z = 123.502
Alpha = 90.000 Beta = 90.000 Gamma = 90.000
NFFT1 = 256 NFFT2 = 128 NFFT3 = 128
Cutoff= 8.000 Tol =0.100E-04
Ewald Coefficient = 0.34864
Interpolation order = 4
--------------------------------------------------------------------------------
3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------
begin time read from input coords = 20.020 ps
Number of triangulated 3-point waters found: 105855
Sum of charges from parm topology file = 0.00000000
Forcing neutrality...
| Dynamic Memory, Types Used:
| Reals 15649305
| Integers 18277903
| Nonbonded Pairs Initial Allocation: 68247918
| GPU memory information (estimate):
| KB of GPU memory in use: 895638
| KB of CPU memory in use: 448464
--------------------------------------------------------------------------------
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
|---------------------------------------------------
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| MC Barostat: Decreasing size of volume moves
check COM velocity, temp: 0.000589 0.00(Removed)
NSTEP = 1000 TIME(PS) = 22.020 TEMP(K) = 300.40 PRESS =
0.0
Etot = -443245.2458 EKtot = 258135.2031 EPtot =
-701380.4489
BOND = 20679.5493 ANGLE = 54023.0417 DIHED =
23639.6058
1-4 NB = 21691.1816 1-4 EEL = 742069.3050 VDWAALS =
96766.7985
EELEC = -1660249.9308 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME =
3987782.5027
Density =
1.0866
------------------------------------------------------------------------------
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| MC Barostat: Decreasing size of volume moves
check COM velocity, temp: 0.000008 0.00(Removed)
NSTEP = 2000 TIME(PS) = 24.020 TEMP(K) = 299.19 PRESS =
0.0
Etot = -443235.5829 EKtot = 257098.3594 EPtot =
-700333.9423
BOND = 20565.2372 ANGLE = 54204.1891 DIHED =
23594.0464
1-4 NB = 21706.4872 1-4 EEL = 741830.2738 VDWAALS =
97102.2262
EELEC = -1659336.4022 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME =
3987782.5027
Density =
1.0866
------------------------------------------------------------------------------
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| MC Barostat: Decreasing size of volume moves
check COM velocity, temp: 0.000013 0.00(Removed)
NSTEP = 3000 TIME(PS) = 26.020 TEMP(K) = 299.88 PRESS =
0.0
Etot = -443239.1740 EKtot = 257684.0000 EPtot =
-700923.1740
BOND = 20388.4613 ANGLE = 54052.9190 DIHED =
23593.7124
1-4 NB = 21723.3563 1-4 EEL = 741912.6123 VDWAALS =
97405.1247
EELEC = -1659999.3600 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME =
3987782.5027
Density =
1.0866
------------------------------------------------------------------------------
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Succeeded
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Succeeded
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| MC Barostat: Decreasing size of volume moves
check COM velocity, temp: 0.000016 0.00(Removed)
NSTEP = 4000 TIME(PS) = 28.020 TEMP(K) = 300.72 PRESS =
0.0
Etot = -443251.6570 EKtot = 258409.7969 EPtot =
-701661.4538
BOND = 20402.5563 ANGLE = 53916.7519 DIHED =
23587.6098
1-4 NB = 21732.2500 1-4 EEL = 742120.1837 VDWAALS =
96905.9092
EELEC = -1660326.7147 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME =
3986435.1378
Density =
1.0870
------------------------------------------------------------------------------
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| MC Barostat: Decreasing size of volume moves
check COM velocity, temp: 0.000016 0.00(Removed)
NSTEP = 5000 TIME(PS) = 30.020 TEMP(K) = 300.59 PRESS =
0.0
Etot = -443275.0487 EKtot = 258301.0313 EPtot =
-701576.0800
BOND = 20323.8904 ANGLE = 53658.5577 DIHED =
23643.9138
1-4 NB = 21879.9182 1-4 EEL = 742301.3063 VDWAALS =
96691.9361
EELEC = -1660075.6025 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME =
3986435.1378
Density =
1.0870
------------------------------------------------------------------------------
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Succeeded
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| MC Barostat: Decreasing size of volume moves
check COM velocity, temp: 0.000024 0.00(Removed)
NSTEP = 6000 TIME(PS) = 32.020 TEMP(K) = 300.34 PRESS =
0.0
Etot = -443269.1771 EKtot = 258087.6875 EPtot =
-701356.8646
BOND = 20212.6686 ANGLE = 53806.5706 DIHED =
23581.7975
1-4 NB = 21906.8206 1-4 EEL = 742536.5967 VDWAALS =
97251.9190
EELEC = -1660653.2376 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME =
3985398.3205
Density =
1.0873
------------------------------------------------------------------------------
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| MC Barostat: Decreasing size of volume moves
check COM velocity, temp: 0.000020 0.00(Removed)
NSTEP = 7000 TIME(PS) = 34.020 TEMP(K) = 299.97 PRESS =
0.0
Etot = -443256.4195 EKtot = 257769.6406 EPtot =
-701026.0601
BOND = 20563.9000 ANGLE = 53882.6825 DIHED =
23605.4296
1-4 NB = 21784.7261 1-4 EEL = 742127.0838 VDWAALS =
96028.8801
EELEC = -1659018.7621 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME =
3985398.3205
Density =
1.0873
------------------------------------------------------------------------------
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| MC Barostat: Decreasing size of volume moves
check COM velocity, temp: 0.000009 0.00(Removed)
NSTEP = 8000 TIME(PS) = 36.020 TEMP(K) = 300.10 PRESS =
0.0
Etot = -443215.7570 EKtot = 257874.9531 EPtot =
-701090.7101
BOND = 20231.0028 ANGLE = 53924.1752 DIHED =
23657.3029
1-4 NB = 21745.9175 1-4 EEL = 741950.4065 VDWAALS =
96280.4326
EELEC = -1658879.9476 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME =
3985398.3205
Density =
1.0873
------------------------------------------------------------------------------
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| MC Barostat: Decreasing size of volume moves
check COM velocity, temp: 0.000014 0.00(Removed)
NSTEP = 9000 TIME(PS) = 38.020 TEMP(K) = 300.20 PRESS =
0.0
Etot = -443216.4543 EKtot = 257959.8594 EPtot =
-701176.3137
BOND = 20231.4366 ANGLE = 53762.8916 DIHED =
23636.0501
1-4 NB = 21757.1156 1-4 EEL = 742345.7271 VDWAALS =
96612.6382
EELEC = -1659522.1730 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME =
3985398.3205
Density =
1.0873
------------------------------------------------------------------------------
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| MC Barostat: Decreasing size of volume moves
check COM velocity, temp: 0.000015 0.00(Removed)
NSTEP = 10000 TIME(PS) = 40.020 TEMP(K) = 300.21 PRESS =
0.0
Etot = -443211.1844 EKtot = 257974.5469 EPtot =
-701185.7313
BOND = 20200.0014 ANGLE = 53993.9041 DIHED =
23582.3879
1-4 NB = 21725.9070 1-4 EEL = 742516.9874 VDWAALS =
95496.7797
EELEC = -1658701.6988 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME =
3985398.3205
Density =
1.0873
------------------------------------------------------------------------------
A V E R A G E S O V E R 10 S T E P S
NSTEP = 10000 TIME(PS) = 40.020 TEMP(K) = 300.16 PRESS =
0.0
Etot = -443241.5701 EKtot = 257929.5078 EPtot =
-701171.0779
BOND = 20379.8704 ANGLE = 53922.5684 DIHED =
23612.1856
1-4 NB = 21765.3680 1-4 EEL = 742171.0483 VDWAALS =
96654.2644
EELEC = -1659676.3829 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME =
3986320.9386
Density =
1.0870
------------------------------------------------------------------------------
R M S F L U C T U A T I O N S
NSTEP = 10000 TIME(PS) = 40.020 TEMP(K) = 0.41 PRESS =
0.0
Etot = 21.1677 EKtot = 349.0851 EPtot =
356.7677
BOND = 163.1750 ANGLE = 148.9182 DIHED =
27.3768
1-4 NB = 68.8050 1-4 EEL = 233.9338 VDWAALS =
554.2039
EELEC = 642.3375 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME =
1033.9590
Density =
0.0003
------------------------------------------------------------------------------
| MC Barostat: 100 volume changes attempted.
| MC Barostat: 3 changes successful ( 3.00%)
------------------------------------------------------------------------------
--------------------------------------------------------------------------------
5. TIMINGS
--------------------------------------------------------------------------------
| NonSetup CPU Time in Major Routines:
|
| Routine Sec %
| ------------------------------
| Nonbond 14.30 4.32
| Bond 0.00 0.00
| Angle 0.00 0.00
| Dihedral 0.00 0.00
| Shake 0.09 0.03
| RunMD 310.46 93.86
| Other 5.90 1.78
| ------------------------------
| Total 330.75
| PME Nonbond Pairlist CPU Time:
|
| Routine Sec %
| ---------------------------------
| Set Up Cit 0.00 0.00
| Build List 0.00 0.00
| ---------------------------------
| Total 0.00 0.00
| PME Direct Force CPU Time:
|
| Routine Sec %
| ---------------------------------
| NonBonded Calc 0.00 0.00
| Exclude Masked 0.00 0.00
| Other 0.01 0.00
| ---------------------------------
| Total 0.01 0.00
| PME Reciprocal Force CPU Time:
|
| Routine Sec %
| ---------------------------------
| 1D bspline 0.00 0.00
| Grid Charges 0.00 0.00
| Scalar Sum 0.00 0.00
| Gradient Sum 0.00 0.00
| FFT 0.00 0.00
| ---------------------------------
| Total 0.00 0.00
| Final Performance Info:
| -----------------------------------------------------
| Average timings for last 1000 steps:
| Elapsed(s) = 36.64 Per Step(ms) = 36.64
| ns/day = 4.72 seconds/ns = 18321.35
|
| Average timings for all steps:
| Elapsed(s) = 330.38 Per Step(ms) = 33.04
| ns/day = 5.23 seconds/ns = 16518.97
| -----------------------------------------------------
| Setup CPU time: 4.74 seconds
| NonSetup CPU time: 330.75 seconds
| Total CPU time: 335.49 seconds 0.09 hours
| Setup wall time: 5 seconds
| NonSetup wall time: 330 seconds
| Total wall time: 335 seconds 0.09 hours
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| MC Barostat: Decreasing size of volume moves
check COM velocity, temp: 0.000016 0.00(Removed)
NSTEP = 5000 TIME(PS) = 30.020 TEMP(K) = 300.59 PRESS =
0.0
Etot = -443275.0487 EKtot = 258301.0313 EPtot =
-701576.0800
BOND = 20323.8904 ANGLE = 53658.5577 DIHED =
23643.9138
1-4 NB = 21879.9182 1-4 EEL = 742301.3063 VDWAALS =
96691.9361
EELEC = -1660075.6025 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME =
3986435.1378
Density =
1.0870
------------------------------------------------------------------------------
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Succeeded
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| MC Barostat: Decreasing size of volume moves
check COM velocity, temp: 0.000024 0.00(Removed)
NSTEP = 6000 TIME(PS) = 32.020 TEMP(K) = 300.34 PRESS =
0.0
Etot = -443269.1771 EKtot = 258087.6875 EPtot =
-701356.8646
BOND = 20212.6686 ANGLE = 53806.5706 DIHED =
23581.7975
1-4 NB = 21906.8206 1-4 EEL = 742536.5967 VDWAALS =
97251.9190
EELEC = -1660653.2376 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME =
3985398.3205
Density =
1.0873
------------------------------------------------------------------------------
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| MC Barostat: Decreasing size of volume moves
check COM velocity, temp: 0.000020 0.00(Removed)
NSTEP = 7000 TIME(PS) = 34.020 TEMP(K) = 299.97 PRESS =
0.0
Etot = -443256.4195 EKtot = 257769.6406 EPtot =
-701026.0601
BOND = 20563.9000 ANGLE = 53882.6825 DIHED =
23605.4296
1-4 NB = 21784.7261 1-4 EEL = 742127.0838 VDWAALS =
96028.8801
EELEC = -1659018.7621 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME =
3985398.3205
Density =
1.0873
------------------------------------------------------------------------------
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| MC Barostat: Decreasing size of volume moves
check COM velocity, temp: 0.000009 0.00(Removed)
NSTEP = 8000 TIME(PS) = 36.020 TEMP(K) = 300.10 PRESS =
0.0
Etot = -443215.7570 EKtot = 257874.9531 EPtot =
-701090.7101
BOND = 20231.0028 ANGLE = 53924.1752 DIHED =
23657.3029
1-4 NB = 21745.9175 1-4 EEL = 741950.4065 VDWAALS =
96280.4326
EELEC = -1658879.9476 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME =
3985398.3205
Density =
1.0873
------------------------------------------------------------------------------
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| MC Barostat: Decreasing size of volume moves
check COM velocity, temp: 0.000014 0.00(Removed)
NSTEP = 9000 TIME(PS) = 38.020 TEMP(K) = 300.20 PRESS =
0.0
Etot = -443216.4543 EKtot = 257959.8594 EPtot =
-701176.3137
BOND = 20231.4366 ANGLE = 53762.8916 DIHED =
23636.0501
1-4 NB = 21757.1156 1-4 EEL = 742345.7271 VDWAALS =
96612.6382
EELEC = -1659522.1730 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME =
3985398.3205
Density =
1.0873
------------------------------------------------------------------------------
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| MC Barostat: Decreasing size of volume moves
check COM velocity, temp: 0.000015 0.00(Removed)
NSTEP = 10000 TIME(PS) = 40.020 TEMP(K) = 300.21 PRESS =
0.0
Etot = -443211.1844 EKtot = 257974.5469 EPtot =
-701185.7313
BOND = 20200.0014 ANGLE = 53993.9041 DIHED =
23582.3879
1-4 NB = 21725.9070 1-4 EEL = 742516.9874 VDWAALS =
95496.7797
EELEC = -1658701.6988 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME =
3985398.3205
Density =
1.0873
------------------------------------------------------------------------------
A V E R A G E S O V E R 10 S T E P S
NSTEP = 10000 TIME(PS) = 40.020 TEMP(K) = 300.16 PRESS =
0.0
Etot = -443241.5701 EKtot = 257929.5078 EPtot =
-701171.0779
BOND = 20379.8704 ANGLE = 53922.5684 DIHED =
23612.1856
1-4 NB = 21765.3680 1-4 EEL = 742171.0483 VDWAALS =
96654.2644
EELEC = -1659676.3829 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME =
3986320.9386
Density =
1.0870
------------------------------------------------------------------------------
R M S F L U C T U A T I O N S
NSTEP = 10000 TIME(PS) = 40.020 TEMP(K) = 0.41 PRESS =
0.0
Etot = 21.1677 EKtot = 349.0851 EPtot =
356.7677
BOND = 163.1750 ANGLE = 148.9182 DIHED =
27.3768
1-4 NB = 68.8050 1-4 EEL = 233.9338 VDWAALS =
554.2039
EELEC = 642.3375 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME =
1033.9590
Density =
0.0003
------------------------------------------------------------------------------
| MC Barostat: 100 volume changes attempted.
| MC Barostat: 3 changes successful ( 3.00%)
------------------------------------------------------------------------------
--------------------------------------------------------------------------------
5. TIMINGS
--------------------------------------------------------------------------------
| NonSetup CPU Time in Major Routines:
|
| Routine Sec %
| ------------------------------
| Nonbond 14.30 4.32
| Bond 0.00 0.00
| Angle 0.00 0.00
| Dihedral 0.00 0.00
| Shake 0.09 0.03
| RunMD 310.46 93.86
| Other 5.90 1.78
| ------------------------------
| Total 330.75
| PME Nonbond Pairlist CPU Time:
|
| Routine Sec %
| ---------------------------------
| Set Up Cit 0.00 0.00
| Build List 0.00 0.00
| ---------------------------------
| Total 0.00 0.00
| PME Direct Force CPU Time:
|
| Routine Sec %
| ---------------------------------
| NonBonded Calc 0.00 0.00
| Exclude Masked 0.00 0.00
| Other 0.01 0.00
| ---------------------------------
| Total 0.01 0.00
| PME Reciprocal Force CPU Time:
|
| Routine Sec %
| ---------------------------------
| 1D bspline 0.00 0.00
| Grid Charges 0.00 0.00
| Scalar Sum 0.00 0.00
| Gradient Sum 0.00 0.00
| FFT 0.00 0.00
| ---------------------------------
| Total 0.00 0.00
| Final Performance Info:
| -----------------------------------------------------
| Average timings for last 1000 steps:
| Elapsed(s) = 36.64 Per Step(ms) = 36.64
| ns/day = 4.72 seconds/ns = 18321.35
|
| Average timings for all steps:
| Elapsed(s) = 330.38 Per Step(ms) = 33.04
| ns/day = 5.23 seconds/ns = 16518.97
| -----------------------------------------------------
| Setup CPU time: 4.74 seconds
| NonSetup CPU time: 330.75 seconds
| Total CPU time: 335.49 seconds 0.09 hours
| Setup wall time: 5 seconds
| NonSetup wall time: 330 seconds
| Total wall time: 335 seconds 0.09 hours
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Received on Thu Jul 24 2014 - 07:30:02 PDT
