amber5 and 77000 atoms ...

From: A. Ababou <axa42_at_psu.edu>
Date: Wed 4 Jul 2001 14:20:38 -0400

Dear amber users,

for my problem, Bill suggested to me to put the "mdin" and the "mdout" for
more clarity about my problem ...so please here you find them included in
the output file ... this a full direct run without previous equilibration,
and about my NFFTX,NFFTY,NFFTZ for the Ewald stuff dont blame my numbers
they are not power of 2,3 or 5 ...thanks alot.

-Ababou

=================================================

          -------------------------------------------------------
          Amber 5 SANDER Scripps/UCSF 1997
          -------------------------------------------------------

| Run at 11: 9:30 on 4 day of
month 7, 19 1
  [-O]verwriting output

File Assignments:
|MDIN : mdp_direct200.in
|MDOUT: A65GAI0W_MD200.out
|INPCR: A65GAI0W6.crd
|PARM : A65GAI0W6.top
|RESTR: A65GAI0W_MD200.xyz
|REFC : refc
|MDVEL: A65GAI0W_MD200.vel
|MDEN : A65GAI0W_MD200.ene
|MDCRD: A65GAI0W_MD200.crd
|MDINF: MD_info200


 Here is the input file:

Molecular Dynamics at constant T and P --> A.A. 7/04/01 run for <=> 200ps
 &cntrl

        TIMLIM =9999999999999,IMIN =0, NMROPT =0,

        NTX =1, IREST =0, NTRX =1,

        NTXO =1, NTPR =50, NTWR =100,
        NTWX =1000, NTWV =1000, NTWE =1000,
        NTWXM =0, NTWVM =0, NTWEM =0,
        IOUTFM =0, NTWPRT =0,

        NTF =3, NTB =2, IDIEL =1,
        DIELC =1, CUT =9.0, NTNB =1,
        NSNB =25, NTID =0, SCNB =2.0,
        SCEE =1.2, CUT2ND =0.0,

        ISFTRP =0, RWELL =0.0,

        NTR =0,

        NRUN =134, NSTLIM =1000, NDFMIN =0,
        NTCM =0, NSCM =0, INIT =3,
        T =0.0, DT =0.0015,

        TEMP0 =300.0, TEMPI =0.0, HEAT =0.0,
        NTT =5, ISOLVP =0,
        TAUTP =0.5, TAUTS =0.2,

        TAUV0 =0.0, TAUV =0.1, VZERO =0.0,

        NTP =1, PRES0 =1.0, COMP =44.6,
        TAUP =1.0, NPSCAL =0,

        NTC =3, TOL =0.00005,

        IBELLY =1,

        IMGSLT =0, IFTRES =1, JFASTW =0,
        IEWALD =1,
 &end
104.284 96.704 103.350 90.0 90.0 90.0
110 110 110 4 0 0 0
0.000005
Group for Belly
RES 25
END
Group for Belly
RES 41 43
END
Group for Belly
RES 57 64
END
Group for Belly
RES 79 86
END
Group for Belly
RES 96
END
Group for Belly
RES 120 124
END
Group for Belly
RES 138 141
END
Group for Belly
RES 213
END
Group for Belly
RES 238
END
Group for Belly
RES 254 256
END
Group for Belly
RES 270 277
END
Group for Belly
RES 292 299
END
Group for Belly
RES 309
END
Group for Belly
RES 333 337
END
Group for Belly
RES 351 354
END
Group for Belly
RES 451
END
Group for Belly
RES 467 469
END
Group for Belly
RES 483 490
END
Group for Belly
RES 505 512
END
Group for Belly
RES 522
END
Group for Belly
RES 546 550
END
Group for Belly
RES 564 567
END
Group for Belly
RES 639 22285
END
END
----------------------------------------------------------------------------

---
Molecular Dynamics at constant T and P --> A.A. 7/04/01 run for <=> 200ps
| Reading &cntrl namelist w/ portable lib
   1.  RESOURCE   USE:
   EWALD SPECIFIC INPUT:
|    Using the SGI specific (ZFFT3D) Fast Fourier Transform
     Box X =  104.284   Box Y =   96.704   Box Z =  103.350
     Alpha =   90.000   Beta  =   90.000   Gamma =   90.000
     NFFT1 =  110       NFFT2 =  110       NFFT3 =  110
     Cutoff=    9.000   Tol   =0.500E-05
     Interpolation order =    4
     Largest sphere to fit in unit cell has radius =    48.352
     Ewald Coefficient =  0.32057
 NATOM  =   76226 NTYPES =      18 NBONH =   69711 MBONA  =    5967
 NTHETH =   13656 MTHETA =    7779 NPHIH =   23777 MPHIA  =   12075
 NHPARM =       0 NPARM  =       0 NNB   =  148947 NRES   =   22285
 NBONA  =    5967 NTHETA =    7779 NPHIA =   12075 NUMBND =      47
 NUMANG =      95 NPTRA  =      34 NATYP =      34 NPHB   =       1
 IFBOX  =       1 NMXRS  =      24 IFCAP =       0
   EWALD MEMORY USE:
|    Total heap storage needed        =       1096
|    Total stack storage needed       =    4793365
|    Adjacent nonbond minimum mask    =     148947
|    Max number of pointers           =         25
|    List build maxmask               =     297894
|    Maximage                         =     183295
   EWALD LOCMEM POINTER OFFSETS
|      Real memory needed by PME        =    4794461
|      Size of ERFTABLE                 =      43276
|      Real memory needed by ERFTABLE   =     216380
|      Integer memory needed by ADJ     =     297894
|      Integer memory used by local nonb=    3204000
|      Real memory used by local nonb   =    1936379
|    MAX NONBOND PAIRS =   20000000
|     Memory Use     Allocated         Used
|     Real            11000000      9690844
|     Hollerith        1000000       632095
|     Integer         10000000      5141937 (static)
|     Max Nonbonded Pairs:20000000
     BOX TYPE: RECTILINEAR
   2.  CONTROL  DATA  FOR  THE  RUN
     TIMLIM=*********   IREST =    0       IBELLY=    1
     KFORM =    1       ICHDNA=    0       IMIN  =    0
     IPOL  =    0       IEWALD=    1
     NTX   =    1       NTXO  =    1
     IG    =    71277   TEMPI =     0.00   HEAT  =    0.000
     NTB   =    2       IFTRES=    1       BOXX  =  104.284
     BOXY  =   96.704   BOXZ  =  103.350
     NRUN  =  134       NTT   =    5       TEMP0 =  300.000
     DTEMP =    0.000   TAUTP =    0.500   TAUTS =    0.200
     ISOLVP=    0       VLIMIT=    0.000
     NTP   =    1       PRES0 =    1.000   COMP  =   44.600
     TAUP  =    1.000   NPSCAL=    0
     NTCM  =    0       NSCM  = 9999999
     NSTLIM= 1000       INIT  =    3       NTU   =    1
     T     =    0.000   DT    =   0.00150
     NTC   =    3       TOL   =   0.00005  JFASTW =    0
     NTF   =    3       NTID  =    0       NTNB  =    1
     NSNB  =   25       IDIEL =    1       IMGSLT=    0
     IPRR  =    0       IPRW  =    0       ITRSLU=    1
     CUT   =    9.000   SCNB  =    2.000
     SCEE  =    1.200   DIELC =    1.000
     CUT2ND=   0.00000
     NTPR  =      50    NTWR  =     100    NTWX  =    1000
     NTWV  =    1000    NTWE  =    1000    NTWXM = 9999999
     NTWVM = 9999999    NTWEM = 9999999    IOUTFM=       0
     NTWPRT=       0    NTWPR0=       0
     NTR   =    0       NTRX  =    1
     TAUR  =   0.00000     NMROPT=    0     ISFTRP=    0
     RWELL =   0.00000     PENCUT=   0.10000
     IVCAP =    0       MATCAP=    0       FCAP  =    1.500
   OTHER DATA:
     IFCAP =    0       NATCAP=    0       CUTCAP=    0.000
     XCAP  =    0.000   YCAP  =    0.000   ZCAP  =    0.000
     NATOM =   76226  NRES =  22285
     Water definition for fast triangulated model:
     Resname = WAT ; Oxygen_name = O   ; Hyd1_name = H1  ; Hyd2_name = H2
Warning: Although EWALD will work with belly
(for equilibration), it is not strictly correct!
(iewald = 1)
       **************************************************
       *                                                *
       *       EXPERIMENTAL EWALD OPTION REQUESTED      *
       *                                                *
       *       Note that this option is new and not     *
       *         tested as extensively on as many       *
       *         machines as the rest of this code      *
       *                                                *
       **************************************************
    LOADING THE BELLY ATOMS AS GROUPS
    ----- READING GROUP     1; TITLE:
 Group for Belly
 GRP    1 RES   25 TO    25
      Number of atoms in this group  =    10
    ----- READING GROUP     2; TITLE:
 Group for Belly
 GRP    2 RES   41 TO    43
      Number of atoms in this group  =    41
    ----- READING GROUP     3; TITLE:
 Group for Belly
 GRP    3 RES   57 TO    64
      Number of atoms in this group  =   102
    ----- READING GROUP     4; TITLE:
 Group for Belly
 GRP    4 RES   79 TO    86
      Number of atoms in this group  =   129
    ----- READING GROUP     5; TITLE:
 Group for Belly
 GRP    5 RES   96 TO    96
      Number of atoms in this group  =    14
    ----- READING GROUP     6; TITLE:
 Group for Belly
 GRP    6 RES  120 TO   124
      Number of atoms in this group  =    71
    ----- READING GROUP     7; TITLE:
 Group for Belly
 GRP    7 RES  138 TO   141
      Number of atoms in this group  =    78
    ----- READING GROUP     8; TITLE:
 Group for Belly
 GRP    8 RES  213 TO   213
      Number of atoms in this group  =     1
    ----- READING GROUP     9; TITLE:
 Group for Belly
 GRP    9 RES  238 TO   238
      Number of atoms in this group  =    10
    ----- READING GROUP    10; TITLE:
 Group for Belly
 GRP   10 RES  254 TO   256
      Number of atoms in this group  =    41
    ----- READING GROUP    11; TITLE:
 Group for Belly
 GRP   11 RES  270 TO   277
      Number of atoms in this group  =   102
    ----- READING GROUP    12; TITLE:
 Group for Belly
 GRP   12 RES  292 TO   299
      Number of atoms in this group  =   129
    ----- READING GROUP    13; TITLE:
 Group for Belly
 GRP   13 RES  309 TO   309
      Number of atoms in this group  =    14
    ----- READING GROUP    14; TITLE:
 Group for Belly
 GRP   14 RES  333 TO   337
      Number of atoms in this group  =    71
    ----- READING GROUP    15; TITLE:
 Group for Belly
 GRP   15 RES  351 TO   354
      Number of atoms in this group  =    78
    ----- READING GROUP    16; TITLE:
 Group for Belly
 GRP   16 RES  451 TO   451
      Number of atoms in this group  =    10
    ----- READING GROUP    17; TITLE:
 Group for Belly
 GRP   17 RES  467 TO   469
      Number of atoms in this group  =    41
    ----- READING GROUP    18; TITLE:
 Group for Belly
 GRP   18 RES  483 TO   490
      Number of atoms in this group  =   102
    ----- READING GROUP    19; TITLE:
 Group for Belly
 GRP   19 RES  505 TO   512
      Number of atoms in this group  =   129
    ----- READING GROUP    20; TITLE:
 Group for Belly
 GRP   20 RES  522 TO   522
      Number of atoms in this group  =    14
    ----- READING GROUP    21; TITLE:
 Group for Belly
 GRP   21 RES  546 TO   550
      Number of atoms in this group  =    71
    ----- READING GROUP    22; TITLE:
 Group for Belly
 GRP   22 RES  564 TO   567
      Number of atoms in this group  =    78
    ----- READING GROUP    23; TITLE:
 Group for Belly
 GRP   23 RES  639 TO 22285
      Number of atoms in this group  = 66867
    ----- END OF GROUP READ -----
   3.  ATOMIC COORDINATES AND VELOCITIES
 begin time read from input coords =     0.000 ps
 Number of triangulated 3-point waters found:    20996
 Using    20996 waters for fast wat-wat
 Solute/solvent pointers:
     IPTSOL= 1286       NATRCM=13229
     IPTRES=    0       IPTATM=    0
     NSPSOL=  654       NSPSTR=13229
     NSOLUT=13229       NATOM =76226
   KE Trans =     0.0000   KE Rot =     0.0000   C.O.M. Vel =    0.000000
     Sum of of charges from parm topology file =  -0.00000019
     Forcing neutrality...
     Total number of mask terms =     126096
     Total number of mask terms =     252192
|    Total Ewald setup time =   0.15063477
 ---------------------------------------------------------------------------
---
 NSTEP =     0  TIME(PS) =    0.000  TEMP(K) =     0.00  PRESS =   2204.28
 Etot   = -250087.9977  EKtot   =       0.0000  EPtot      = -250087.9977
 BOND   =       0.0000  ANGLE   =    4215.4649  DIHED      =   12853.9687
 1-4 NB =     383.6088  1-4 EEL = -134013.5342  VDWAALS    =   21590.6622
 EELEC  = -155118.1681  EHBOND  =       0.0000  CONSTRAINT =       0.0000
 EKCMT  =       0.0000  VIRIAL  =  -49604.0475  VOLUME     = 1042251.6714
 T_SOLUTE =     0.0000  T_SOLVENT =     0.0000
                                                Density    =       0.7621
 Ewald error estimate:   0.7658E-03
 ---------------------------------------------------------------------------
---
     COORDINATE RESETTING CANNOT BE ACCOMPLISHED,
     DEVIATION IS TOO LARGE
     NITER, NIT, LL, I AND J ARE :    0    0   96 1177 1178
 FATAL ERROR
=================================================
********************************************
 Dr. A. ABABOU
Penn State University
405 Chandlee Lab
University Park, PA 16802 USA
Tel:   +1 814 - 865 -1273
Fax:   +1 814 - 863 - 8403
e-mail : axa42_at_psu.edu
        (ababou_at_aspirine.u-strasbg.fr)
********************************************

Received on Wed Jul 04 2001 - 11:20:38 PDT