Hi guys,
I want to clarify something in my last e-mail.Energy difference occurs
when i put ibelly into the calculation. If i don't have the ibelly,
everthing is same in nmode and sander. There is probably a difference in
nmode and sander about calculation of number of non-bonded pairs, and we
can solve this difference by taking an infinite cut-off, but what will i
do in the case with ibelly?
thanks in advance
sebnem
<quote who="sebnem">
> 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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Sebnem Essiz
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Received on Wed Aug 17 2005 - 17:53:01 PDT
