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AMBER Archive (2001)
Subject: amber5 and 77000 atoms ...
From: A. Ababou (axa42_at_psu.edu)
Date: Wed Jul 04 2001 - 13:20:38 CDT
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- Previous message: Michal Otyepka: "(no subject)"
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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) ********************************************
- Next message: GUILBAUD Philippe 153683: "RE: CCl4 ESP Grid problem with jaguar"
- Previous message: Michal Otyepka: "(no subject)"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]
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