AMBER Archive (2005)

Subject: AMBER: difference of energy in sander and nmode in amber 7

From: sebnem (sebnem_at_mercury.chem.pitt.edu)
Date: Mon Aug 15 2005 - 16:55:24 CDT

Hi,
I need to carry a molecule from nmode (amber 7), where i carried out NMA
analysis, to sander(amber 7). However when I take the minimized structure
from nmode, i am getting a different non-bonded energy term in sander. I
tried to increase the cutoff as you suggested in previous e-mails, but
there is still the same problem.
I am attaching output files from sander and nmode, input crd and top files
are exactly same for testing the energy terms. I'll really appreciate if
you can help me tu understand why the E-NONB is different in the first
step of these runs.
thanks a lot,
sebnem

Here is the input of nmode:
minimization,
&data
     ntrun=4,
     cut=9999.0
     nprint=100,
     drms=0.00000001,
     maxcyc=2,
     scnb=2.0,
     scee=1.2,
     ibelly=1,
     idiel=1,
&end
 group info
RES 1 34
END
END

Here is the output of nmode
          *******************************************************
          Initiate the NMODE module of AMBER 7
          *******************************************************

  minimization, saving coords in binary
       ntrun maxcyc ibelly drms
          4 2 1 0.10E-07
       rcut scnb scee dielc idiel
   9999.00000 2.00000 1.20000 1.00000 1
      nsave dfpred bdwnhl smx emx alpha ndiag
         20 0.01000 0.10000 0.08000 0.30000 0.80000 10
 ipol = 0
 i3bod = 0
 nvect = 10
| New format PARM file being parsed.
| Version = 1.000 Date = 11/15/04 Time = 17:44:18

    PARM file has the title:

   Memory allocation :

           1 798 1595 1618 1641
        1685 1729 1773 1817 1861
        1892 1923 1954 1973 2064
        2155 2155 2155 2155 5343
           0 1 798 1596 2394
        2564 2843 3124 3405 3686
        3967 4254 4541 4828 5453
        6078 6703 7328 7727 8126
        8525 8924 11195 13466 15737
       18008 20279 22550 24821 27092
       29363 31634 34934 35731 38124
       39720 40518 8531 10922 15704
       41316 0 42114 0 0
           0 0 0 0 36528
       37326 7734 0

     Duplicated 0 dihedrals

     Duplicated 0 dihedrals

   group info
      GROUP 1 CONSISTS OF RESIDUES 1 TO 34

      NUMBER OF ATOMS IN THIS GROUP = 552

  END

     THE GROUP 0 CONTAINS ALL ATOMS NOT DEFINED AS GROUPS BY THE INPUT

   Memory allocation :

           1 798 1595 1618 1641
        1685 1729 1773 1817 1861
        1892 1923 1954 1973 2064
        2155 2155 2155 2155 5343
           0 1 798 1596 2394
        2564 2843 3124 3405 3686
        3967 4254 4541 4828 5453
        6078 6703 7328 7727 8126
        8525 8924 11195 13466 15737
       18008 20279 22550 24821 27092
       29363 31634 34934 35731 38124
       39720 40518 8531 10922 15704
       42114 2780366 42912 0 0
           0 0 0 0 36528
       37326 7734 0

Total memory required : 2782022 real words

Total memory avail : 20000000 real words

Total memory required : 42912 integer words

Total memory avail : 4000000 integer words

Maximum nonbond pairs 3957087

 Getting coordinates from file with title:
       NPRO

    Number of non-bonded pairs = 149048
    Number of H-bonded pairs = 0

 ***************** ***************** *****************
   step = 0
     F = -0.324654E+03 GRDMAX = 0.724669E+01 GNORM = 0.103917E+01
       E-NONB E-ELE E-HBOND E-BOND
    -0.23102E+03 -0.23184E+04 0.00000E+00 0.71846E+01
       E-ANGLE E-DIHED E-NB14 E-EEL14
     0.32864E+02 0.24495E+03 0.11221E+03 0.18276E+04
       E-POL E-3BOD
     0.00000E+00 0.00000E+00
          b1 = -0.00703 b2 = -0.00252 tlamba = -0.10703
          rms of step length = 0.0517483146
          ene @step k-1 = -324.653976 ene @k = -341.009318

 ***************** ***************** *****************
   step = 1
     F = -0.341009E+03 GRDMAX = 0.842043E+01 GNORM = 0.475287E+00
       E-NONB E-ELE E-HBOND E-BOND
    -0.22755E+03 -0.22622E+04 0.00000E+00 0.11221E+02
       E-ANGLE E-DIHED E-NB14 E-EEL14
     0.34543E+02 0.24393E+03 0.10531E+03 0.17538E+04
       E-POL E-3BOD
     0.00000E+00 0.00000E+00
          b1 = 0.00000 b2 = 0.00000 tlamba = -0.10000
          rms of step length = 0.0249393840
          ene @step k-1 = -341.009318 ene @k = -342.182669

 ***************** ***************** *****************
   step = 2
     F = -0.342183E+03 GRDMAX = 0.104181E+01 GNORM = 0.650263E-01
       E-NONB E-ELE E-HBOND E-BOND
    -0.22751E+03 -0.22604E+04 0.00000E+00 0.10424E+02
       E-ANGLE E-DIHED E-NB14 E-EEL14
     0.34949E+02 0.24387E+03 0.10518E+03 0.17513E+04
       E-POL E-3BOD
     0.00000E+00 0.00000E+00
 in savec point = 2

                              F i n a l R e s u l t s :

 ***************** ***************** *****************
   step = 0
     F = -0.342183E+03 GRDMAX = 0.104181E+01 GNORM = 0.650263E-01
       E-NONB E-ELE E-HBOND E-BOND
    -0.22751E+03 -0.22604E+04 0.00000E+00 0.10424E+02
       E-ANGLE E-DIHED E-NB14 E-EEL14
     0.34949E+02 0.24387E+03 0.10518E+03 0.17513E+04
       E-POL E-3BOD
     0.00000E+00 0.00000E+00

| cpu time = 27.55 seconds

***************************************************************************

here is the output for the same files in sander:

          -------------------------------------------------------
          Amber 7 SANDER Scripps/UCSF 2002
          -------------------------------------------------------

| Mon Aug 15 17:24:25 2005

  [-O]verwriting output

File Assignments:
| MDIN: mdmod1.in
| MDOUT: OUT_sander
|INPCRD:trial.crd
|PARM:FINAL.top
|RESTRT:restrt
|REFC:refc
|MDVEL:mdvel
|MDEN:mden
|MDCRD:mdcrd
|MDINFO:mdinfo
|INPDIP:inpdip
|RSTDIP:rstdip

 Here is the input file:

&cntrl
imin = 0, ntb = 0,
  igb = 0, ntpr = 1, ntwx = 1, ntwv=1,
  ntt = 0,intdiel=1,dielc=1,
  tempi = 0.0, temp0 = 0.0,tautp=0.2,
  nstlim = 1, dt = 0.0005,
  cut = 9999,
  scee=1.2,
  scnb=2.0,
  ibelly=1,
 /
group info
RES 1 34
END
END

--------------------------------------------------------------------------------
   1. RESOURCE USE:
--------------------------------------------------------------------------------

| Flags:
| NONPERIODIC ntb=0 and igb=0: Setting up nonperiodic simulation
| *** cutoff > system size, list only builds once
| New format PARM file being parsed.
| Version = 1.000 Date = 11/15/04 Time = 17:44:18
 NATOM = 797 NTYPES = 13 NBONH = 280 MBONA = 286
 NTHETH = 624 MTHETA = 398 NPHIH = 1156 MPHIA = 714
 NHPARM = 0 NPARM = 0 NNB = 3299 NRES = 279
 NBONA = 286 NTHETA = 398 NPHIA = 714 NUMBND = 23
 NUMANG = 44 NPTRA = 31 NATYP = 19 NPHB = 0
 IFBOX = 0 NMXRS = 24 IFCAP = 0 NEXTRA = 0

| Memory Use Allocated Used
| Real 25000000 52293
| Hollerith 400000 5063
| Integer 12500000 1087869

| Max Nonbonded Pairs:********
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals

--------------------------------------------------------------------------------
   2. CONTROL DATA FOR THE RUN
--------------------------------------------------------------------------------

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 =
 500
     iwrap = 0, ntwx = 1, ntwv = 1, ntwe =
   0
     ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat=
   0

Potential function:
     ntf = 1, ntb = 0, igb = 0, nsnb =
  25
     ipol = 0, gbsa = 0
     dielc = 1.00000, cut =9999.00000, intdiel = 1.00000
     scnb = 2.00000, scee = 1.20000

Frozen or restrained atoms:
     ibelly = 1, ntr = 0

Molecular dynamics:
     nstlim = 1, nscm = 9999999, nrespa = 1
     t = 0.00000, dt = 0.00050, vlimit = 20.00000

Warning: Although EWALD will work with belly
(for equilibration), it is not strictly correct!

    LOADING THE BELLY ATOMS AS GROUPS

    ----- READING GROUP 1; TITLE:
 group info
 GRP 1 RES 1 TO 34
      Number of atoms in this group = 552
    ----- END OF GROUP READ -----

--------------------------------------------------------------------------------
   3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------

  NPRO
 begin time read from input coords = 0.000 ps

 Number of triangulated 3-point waters found: 0

     Sum of charges from parm topology file = 0.00003996
     Forcing neutrality...

--------------------------------------------------------------------------------
   4. RESULTS
--------------------------------------------------------------------------------

 ---------------------------------------------------

     eedmeth=4: Setting switch to one everywhere

 ---------------------------------------------------
| Local SIZE OF NONBOND LIST = 284288
| TOTAL SIZE OF NONBOND LIST = 284288

 NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS = 0.0
 Etot = -443.4719 EKtot = 0.0000 EPtot = -443.4719
 BOND = 7.1846 ANGLE = 32.8644 DIHED = 244.9476
 1-4 NB = 112.2092 1-4 EEL = 1827.6101 VDWAALS = -349.8431
 EELEC = -2318.4446 EHBOND = 0.0000 RESTRAINT = 0.0000
 ------------------------------------------------------------------------------

 NSTEP = 1 TIME(PS) = 0.001 TEMP(K) = 0.00 PRESS = 0.0
 Etot = -443.4719 EKtot = 0.0000 EPtot = -443.4719
 BOND = 7.1846 ANGLE = 32.8644 DIHED = 244.9476
 1-4 NB = 112.2092 1-4 EEL = 1827.6101 VDWAALS = -349.8431
 EELEC = -2318.4446 EHBOND = 0.0000 RESTRAINT = 0.0000
 ------------------------------------------------------------------------------

      A V E R A G E S O V E R 1 S T E P S

 NSTEP = 1 TIME(PS) = 0.001 TEMP(K) = 0.00 PRESS = 0.0
 Etot = -443.4719 EKtot = 0.0000 EPtot = -443.4719
 BOND = 7.1846 ANGLE = 32.8644 DIHED = 244.9476
 1-4 NB = 112.2092 1-4 EEL = 1827.6101 VDWAALS = -349.8431
 EELEC = -2318.4446 EHBOND = 0.0000 RESTRAINT = 0.0000
 ------------------------------------------------------------------------------

      R M S F L U C T U A T I O N S

 NSTEP = 1 TIME(PS) = 0.001 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
--------------------------------------------------------------------------------

| Ewald setup time 0.02 (50.00% of List )
| Build the list 0.02 (50.00% of List )
| List time 0.04 (40.00% of Nonbo)
| Direct Ewald time 0.06 (100.0% of Ewald)
| Ewald time 0.06 (60.00% of Nonbo)
| Nonbond force 0.10 (100.0% of Force)
| Force time 0.10 (83.33% of Runmd)
| Other 0.02 (16.67% of Runmd)
| Runmd Time 0.12 (63.16% of Total)
| Other 0.07 (36.84% of Total)
| Total time 0.19 (100.0% of ALL )

| Highest rstack allocated: 3910
| Highest istack allocated: 39888

| Setup wallclock 0 seconds
| Nonsetup wallclock 1 seconds
 *****

Sebnem Essiz

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