Dear David,
Thank you for your answer.
Yes, it is a spherical system (water cap).
Setting eedmeth=4 changes the energies, but still with a difference of 6000 kcal.
With cut=10, the energies still differ by 4000 kcal/mol.
The intention was to use the forces in external QM/MM calculations, but we go for another option.
Best Regards,
Ulf
________________________________
From: David Cerutti <dscerutti.gmail.com>
Sent: 04 November 2016 07:43
To: AMBER Mailing List
Subject: Re: [AMBER] do_debugf changes energy
The forcedump file produced by debugging is a rich source of energies and
so forth; might be worth a look in there to see what you can find.
That said, I'm puzzled by the fact that you have lots of water molecules in
your simulation yet no boundary conditions, like a droplet simulation of
sorts. eedmeth=4 for bare Coulomb interactions, definitely a droplet thing
to do. The last time I looked in the debugf code (which is a long time
ago), there was some shenanigans with the non-bonded pairlist, so a cutoff
of 40A might well be running you into some sort of list building problem.
This would be consistent with the long-ranged electrostatics being quite
different, the long-ranged vdW energy being only mildly different, and all
other components of the system (including 1-4 elec and vdW) matching
exactly. See what you get with debugf and a cutoff of 10A--energies and
forces won't be very good for research purposes, but they might match for
debugging.
Dave
On Fri, Nov 4, 2016 at 2:25 AM, Ulf Ryde <ulf.ryde.teokem.lu.se> wrote:
> 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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>
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Received on Fri Nov 04 2016 - 00:30:03 PDT
