Hi!
Why does do_debugf change the calculated energy?
Below are outputs of two calculations differing only in that
the first uses do_debugf, the other not.
The energy changes by 9000 kcal (electrostatics and vdW).
Is there any way to get the same energy with do_debugf?
Best Regards,
Ulf
*With do_debugf*
-------------------------------------------------------
Amber 16 SANDER 2016
-------------------------------------------------------
| Run on 11/03/2016 at 09:31:48
| Executable path: /temp4/bio/AMBER/Amber16/bin/sander
| Working directory: /home/ulf/Aurora/T/Geng/Rs/A16
| Hostname: Unknown
[-O]verwriting output
File Assignments:
| MDIN: i1
| MDOUT: o13
|INPCRD: prmcrd3
| PARM: prmtop3
|RESTRT: mdrest2
| REFC: refc
| MDVEL: mdvel
| MDFRC: mdfrc
| MDEN: mden2
| MDCRD: mdcrd
|MDINFO: mdinfo
| MTMD: mtmd
|INPDIP: inpdip
|RSTDIP: rstdip
|INPTRA: inptraj
Here is the input file:
FDH 29/11-15
&cntrl
irest=0,ntx=1,
nstlim=1,dt=0.0,
imin=0,maxcyc=1,drms=0.001,
temp0=300.0,ntt=1,tautp=0.2,
ntc=1,ntf=1,
nsnb=25,cut=40.0,dielc=1.0,
ntpr=1,ntwx=0,ntwv=0,ntwe=1,ntxo=1,
ntb=0,ntp=0,taup=0.2,
ibelly=0
&end
&debugf
do_debugf=1
&end
--------------------------------------------------------------------------------
1. RESOURCE USE:
--------------------------------------------------------------------------------
| Flags:
| NONPERIODIC ntb=0 and igb=0: Setting up nonperiodic simulation
|Largest sphere to fit in unit cell has radius = 80.885
| New format PARM file being parsed.
| Version = 1.000 Date = 05/29/02 Time = 12:05:35
NATOM = 57154 NTYPES = 21 NBONH = 49328 MBONA = 8035
NTHETH = 17068 MTHETA = 10949 NPHIH = 35197 MPHIA = 33910
NHPARM = 0 NPARM = 0 NNB = 140340 NRES = 14923
NBONA = 8035 NTHETA = 10949 NPHIA = 33910 NUMBND = 108
NUMANG = 253 NPTRA = 232 NATYP = 58 NPHB = 1
IFBOX = 0 NMXRS = 71 IFCAP = 1 NEXTRA = 0
NCOPY = 0
| Memory Use Allocated
| Real 3779098
| Hollerith 186387
| Integer 4638988
| Max Pairs 1411475184
| nblistReal 685848
| nblist Int 1602526
| Total 1379262 kbytes
| 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
--------------------------------------------------------------------------------
2. CONTROL DATA FOR THE RUN
--------------------------------------------------------------------------------
default_name
General flags:
imin = 0, nmropt = 0
Nature and format of input:
ntx = 1, irest = 0, ntrx = 1
Nature and format of output:
ntxo = 1, ntpr = 1, ntrx = 1, ntwr = 1
iwrap = 0, ntwx = 0, ntwv = 0, ntwe = 1
ioutfm = 1, ntwprt = 0, idecomp = 0, rbornstat= 0
Potential function:
ntf = 1, ntb = 0, igb = 0, nsnb = 25
ipol = 0, gbsa = 0, iesp = 0
dielc = 1.00000, cut = 40.00000, intdiel = 1.00000
Frozen or restrained atoms:
ibelly = 0, ntr = 0
Molecular dynamics:
nstlim = 1, nscm = 1000, nrespa = 1
t = 0.00000, dt = 0.00000, vlimit = 20.00000
Berendsen (weak-coupling) temperature regulation:
temp0 = 300.00000, tempi = 0.00000, tautp = 0.20000
Water cap:
ivcap = 0, natcap = 15349
fcap = 1.50000, cutcap = 53.00000
xcap = 0.00000, ycap = 0.00000, zcap = 0.00000
| INFO: Old style inpcrd file read
--------------------------------------------------------------------------------
3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------
defa
begin time read from input coords = 0.000 ps
Number of triangulated 3-point waters found: 13935
Sum of charges from parm topology file = -0.99907788
DEBUG FORCE!; calling force routine
---------------------------------------------------
eedmeth=4: Setting switch to one everywhere
---------------------------------------------------
| Local SIZE OF NONBOND LIST = 534532550
| TOTAL SIZE OF NONBOND LIST = 534532550
DEBUG FORCE!; back from force routine
NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS = 0.0
Etot = -179891.0536 EKtot = 0.0000 EPtot = -179891.0536
BOND = 903.3345 ANGLE = 2209.6350 DIHED = 11084.1806
1-4 NB = 4381.2705 1-4 EEL = 38031.3586 VDWAALS = 27927.8851
EELEC = -264429.2923 EHBOND = 0.0000 RESTRAINT = 0.5746
EAMBER (non-restraint) = -179891.6281
EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 4259269.0285
Density = 0.1414
------------------------------------------------------------------------------
*Without:*
-------------------------------------------------------
Amber 16 SANDER 2016
-------------------------------------------------------
| Run on 11/03/2016 at 09:30:58
| Executable path: /temp4/bio/AMBER/Amber16/bin/sander
| Working directory: /home/ulf/Aurora/T/Geng/Rs/A16
| Hostname: Unknown
[-O]verwriting output
File Assignments:
| MDIN: i2
| MDOUT: o23
|INPCRD: prmcrd3
| PARM: prmtop3
|RESTRT: mdrest2
| REFC: refc
| MDVEL: mdvel
| MDFRC: mdfrc
| MDEN: mden2
| MDCRD: mdcrd
|MDINFO: mdinfo
| MTMD: mtmd
|INPDIP: inpdip
|RSTDIP: rstdip
|INPTRA: inptraj
Here is the input file:
FDH 29/11-15
&cntrl
irest=0,ntx=1,
nstlim=1,dt=0.0,
imin=0,maxcyc=1,drms=0.001,
temp0=300.0,ntt=1,tautp=0.2,
ntc=1,ntf=1,
nsnb=25,cut=40.0,dielc=1.0,
ntpr=1,ntwx=0,ntwv=0,ntwe=1,ntxo=1,
ntb=0,ntp=0,taup=0.2,
ibelly=0
&end
--------------------------------------------------------------------------------
1. RESOURCE USE:
--------------------------------------------------------------------------------
| Flags:
| NONPERIODIC ntb=0 and igb=0: Setting up nonperiodic simulation
|Largest sphere to fit in unit cell has radius = 80.885
| New format PARM file being parsed.
| Version = 1.000 Date = 05/29/02 Time = 12:05:35
NATOM = 57154 NTYPES = 21 NBONH = 49328 MBONA = 8035
NTHETH = 17068 MTHETA = 10949 NPHIH = 35197 MPHIA = 33910
NHPARM = 0 NPARM = 0 NNB = 140340 NRES = 14923
NBONA = 8035 NTHETA = 10949 NPHIA = 33910 NUMBND = 108
NUMANG = 253 NPTRA = 232 NATYP = 58 NPHB = 1
IFBOX = 0 NMXRS = 71 IFCAP = 1 NEXTRA = 0
NCOPY = 0
| Memory Use Allocated
| Real 3779098
| Hollerith 186387
| Integer 4638988
| Max Pairs 1411475184
| nblistReal 685848
| nblist Int 1602526
| Total 1379262 kbytes
| 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
--------------------------------------------------------------------------------
2. CONTROL DATA FOR THE RUN
--------------------------------------------------------------------------------
default_name
General flags:
imin = 0, nmropt = 0
Nature and format of input:
ntx = 1, irest = 0, ntrx = 1
Nature and format of output:
ntxo = 1, ntpr = 1, ntrx = 1, ntwr = 1
iwrap = 0, ntwx = 0, ntwv = 0, ntwe = 1
ioutfm = 1, ntwprt = 0, idecomp = 0, rbornstat= 0
Potential function:
ntf = 1, ntb = 0, igb = 0, nsnb = 25
ipol = 0, gbsa = 0, iesp = 0
dielc = 1.00000, cut = 40.00000, intdiel = 1.00000
Frozen or restrained atoms:
ibelly = 0, ntr = 0
Molecular dynamics:
nstlim = 1, nscm = 1000, nrespa = 1
t = 0.00000, dt = 0.00000, vlimit = 20.00000
Berendsen (weak-coupling) temperature regulation:
temp0 = 300.00000, tempi = 0.00000, tautp = 0.20000
Water cap:
ivcap = 0, natcap = 15349
fcap = 1.50000, cutcap = 53.00000
xcap = 0.00000, ycap = 0.00000, zcap = 0.00000
| INFO: Old style inpcrd file read
--------------------------------------------------------------------------------
3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------
defa
begin time read from input coords = 0.000 ps
Number of triangulated 3-point waters found: 13935
Sum of charges from parm topology file = -0.99907788
--------------------------------------------------------------------------------
4. RESULTS
--------------------------------------------------------------------------------
| # of SOLUTE degrees of freedom (RNDFP): 171462.
| # of SOLVENT degrees of freedom (RNDFS): 0.
| NDFMIN = 171456. NUM_NOSHAKE = 0 CORRECTED RNDFP = 171456.
| TOTAL # of degrees of freedom (RNDF) = 171456.
---------------------------------------------------
eedmeth=4: Setting switch to one everywhere
---------------------------------------------------
| Local SIZE OF NONBOND LIST = 534532550
| TOTAL SIZE OF NONBOND LIST = 534532550
NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS = 0.0
Etot = -188813.0143 EKtot = 0.0000 EPtot = -188813.0143
BOND = 903.3345 ANGLE = 2209.6350 DIHED = 11084.1806
1-4 NB = 4381.2705 1-4 EEL = 38031.3586 VDWAALS = 27929.1658
EELEC = -273352.5338 EHBOND = 0.0000 RESTRAINT = 0.5746
EAMBER (non-restraint) = -188813.5889
------------------------------------------------------------------------------
NSTEP = 1 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS = 0.0
Etot = -188813.0143 EKtot = 0.0000 EPtot = -188813.0143
BOND = 903.3345 ANGLE = 2209.6350 DIHED = 11084.1806
1-4 NB = 4381.2705 1-4 EEL = 38031.3586 VDWAALS = 27929.1658
EELEC = -273352.5338 EHBOND = 0.0000 RESTRAINT = 0.5746
EAMBER (non-restraint) = -188813.5889
------------------------------------------------------------------------------
A V E R A G E S O V E R 1 S T E P S
NSTEP = 1 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS = 0.0
Etot = -188813.0143 EKtot = 0.0000 EPtot = -188813.0143
BOND = 903.3345 ANGLE = 2209.6350 DIHED = 11084.1806
1-4 NB = 4381.2705 1-4 EEL = 38031.3586 VDWAALS = 27929.1658
EELEC = -273352.5338 EHBOND = 0.0000 RESTRAINT = 0.5746
EAMBER (non-restraint) = -188813.5889
------------------------------------------------------------------------------
R M S F L U C T U A T I O N S
NSTEP = 1 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS = 0.0
Etot = 0.0000 EKtot = 0.0000 EPtot = 0.0000
BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000
1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 0.0000
EELEC = 0.0000 EHBOND = 0.0000 RESTRAINT = 0.0000
------------------------------------------------------------------------------
--------------------------------------------------------------------------------
5. TIMINGS
--------------------------------------------------------------------------------
| Read coords time 0.05 ( 0.15% of Total)
| Build the list 7.07 (100.0% of List )
| Other 0.00 ( 0.05% of List )
| List time 7.08 (20.38% of Nonbo)
| Short_ene time 27.64 (100.0% of Direc)
| Other 0.00 ( 0.01% of Direc)
| Direct Ewald time 27.65 (100.0% of Ewald)
| Other 0.00 ( 0.01% of Ewald)
| Ewald time 27.65 (79.62% of Nonbo)
| Nonbond force 34.73 (100.0% of Force)
| Bond/Angle/Dihedral 0.03 ( 0.09% of Force)
| Force time 34.76 (99.54% of Runmd)
| Verlet update time 0.14 ( 0.40% of Runmd)
| Other 0.02 ( 0.06% of Runmd)
| Runmd Time 34.92 (98.29% of Total)
| Other 0.55 ( 1.56% of Total)
| Total time 35.53 (100.0% of ALL )
| Number of list builds : 1
| Highest rstack allocated: 111995
| Highest istack allocated: 22399
| Final Performance Info:
| -----------------------------------------------------
| Average timings for all steps:
| Elapsed(s) = 34.92 Per Step(ms) = 34919.61
| ns/day = 0.00 seconds/ns = Infinity
| -----------------------------------------------------
| Job began at 09:30:58.642 on 11/03/2016
| Setup done at 09:30:59.251 on 11/03/2016
| Run done at 09:31:34.170 on 11/03/2016
| wallclock() was called 66 times
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Received on Thu Nov 03 2016 - 23:30:02 PDT
