AMBER Archive (2003)

Subject: Re: AMBER: dynamics of isolated system

From: Dr. Yong Duan (yduan_at_albert.chem.udel.edu)
Date: Tue Jul 29 2003 - 14:04:42 CDT

Just out of curiousity, what system is this, i.e., how many molecules did
you have. Your "isolated" system is not terribly informative.
By the way, did you do energy minimization before your started MD? You had
pretty high VDW energy term, suggesting two (or more) atoms are very
close.
Typically, one start with energy minimization, followed by low tempi. When
tempi=0, the initial v is calculated by taking gradient,

Good luck!

yong
On Tue, 29 Jul 2003, Herbert Georg wrote:

> Hi there,
>
> I'm new to amber and I'm trying to learn how to deal with it....
> Within this spirit, I'm trying to perform a MD of an isolated system at
> room temperature, therefore I have chosen to use the variable NTB=0. All
> of the others are common values, I think.
> But it isn't working as shows the output:
>
>
> -------------------------------------------------------
> Amber 7 SANDER Scripps/UCSF 2002
> -------------------------------------------------------
>
> | Tue Jul 29 15:10:12 2003
>
> [-O]verwriting output
>
> File Assignments:
> | MDIN:
> md0.in
> | MDOUT:
> md0.out
> |INPCRD:
> alphacd.crd
> | PARM:
> alphacd.top
> |RESTRT:
> restrt
> | REFC:
> refc
> | MDVEL:
> md0.vel
> | MDEN:
> md0.en
> | MDCRD:
> md0.crd
> |MDINFO:
> mdinfo
> |INPDIP:
> inpdip
> |RSTDIP:
> rstdip
>
>
> Here is the input file:
>
> # IMIN -> tipo de
> simulacao
> # NTX, IREST -> nature and format of
> input
> # NTWX, NTWV, NTWE, NTWR, NTPR -> nature ando format of
> output
> # NTB -> Periodic
> boundary
> # NSTLIM, NSCM -> MD run
> flags
> # NTT, TEMP0, TAUTP -> Temperature
> regulation
> # NTC ->
> Shake
>
>
> alpha-ciclodextrina isolada a temperatura ambiente
> (equilibracao)
> &cntrl
>
> IMIN=0, IREST=0,
> NTX=1,
> NTWX=50, NTWV=50,
> NTWR=50,
> NTWE=50,
> NTPR=50,
>
> NSTLIM=5000,
> NTB=0,
> NSCM=100,
>
> NTC=1,
> NTT=1, TEMP0=298.15,
> TAUTP=1.0,
> &end
>
>
>
>
>
>
> --------------------------------------------------------------------------------
> 1. RESOURCE USE:
> --------------------------------------------------------------------------------
>
> |
> Flags:
>
> | NONPERIODIC ntb=0 and igb=0: Setting up nonperiodic simulation
> | New format PARM file being parsed.
> | Version = 1.000 Date = 06/17/03 Time = 17:07:40
> NATOM = 126 NTYPES = 6 NBONH = 60 MBONA = 65
> NTHETH = 134 MTHETA = 90 NPHIH = 287 MPHIA = 192
> NHPARM = 0 NPARM = 0 NNB = 661 NRES = 1
> NBONA = 65 NTHETA = 90 NPHIA = 192 NUMBND = 6
> NUMANG = 11 NPTRA = 12 NATYP = 6 NPHB = 0
> IFBOX = 0 NMXRS = 126 IFCAP = 0 NEXTRA = 0
>
>
> | Memory Use Allocated Used
> | Real 2000000 9471
> | Hollerith 400000 759
> | Integer 2000000 418848
>
> | Max Nonbonded Pairs: 5400000
> | Duplicated 0 dihedrals
> | Duplicated 0 dihedrals
>
> --------------------------------------------------------------------------------
> 2. CONTROL DATA FOR THE RUN
> --------------------------------------------------------------------------------
>
> ACD
>
>
> 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 = 50, ntrx = 1, ntwr
> = 50
> iwrap = 0, ntwx = 50, ntwv = 50, ntwe
> = 50
> 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 = 8.00000, intdiel = 1.00000
> scnb = 2.00000, scee = 1.20000
>
> Frozen or restrained atoms:
> ibelly = 0, ntr = 0
>
> Molecular dynamics:
> nstlim = 5000, nscm = 100, nrespa = 1
> t = 0.00000, dt = 0.00100, vlimit = 20.00000
>
> Temperature regulation:
> ig = 71277, ntt = 1, vrand = 0
> temp0 = 298.15000, tempi = 0.00000, heat = 0.00000
> dtemp = 5.00000, tautp = 1.00000
>
> --------------------------------------------------------------------------------
> 3. ATOMIC COORDINATES AND VELOCITIES
> --------------------------------------------------------------------------------
>
> ACD
>
> begin time read from input coords = 0.000 ps
>
> Number of triangulated 3-point waters found: 0
>
> Sum of charges from parm topology file = 0.00200000
> Forcing neutrality...
>
> --------------------------------------------------------------------------------
> 4. RESULTS
> --------------------------------------------------------------------------------
>
> ---------------------------------------------------
>
> eedmeth=4: Setting switch to one everywhere
>
> ---------------------------------------------------
> | Local SIZE OF NONBOND LIST = 5578
> | TOTAL SIZE OF NONBOND LIST = 5578
>
> NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS = 0.0
> Etot = nan EKtot = 0.0000 EPtot = nan
> BOND = 4.0519 ANGLE = nan DIHED = 73.9878
> 1-4 NB = 23.5207 1-4 EEL = 619.4757 VDWAALS = 59562.8837
> EELEC = -389.5910 EHBOND = 0.0000 RESTRAINT = 0.0000
> ------------------------------------------------------------------------------
>
> vlimit exceeded for step 0; vmax = 93.6575435
> vlimit exceeded for step 1; vmax = 20.5330838
> vlimit exceeded for step 2; vmax = 8790956.85
> vlimit exceeded for step 3; vmax = 3218.44947
> vlimit exceeded for step 4; vmax = 186.852475
> vlimit exceeded for step 5; vmax = 281.72415
> vlimit exceeded for step 6; vmax = 305.697176
> vlimit exceeded for step 7; vmax = 302.390465
> vlimit exceeded for step 8; vmax = 221.471003
> vlimit exceeded for step 9; vmax = 178.076931
> vlimit exceeded for step 10; vmax = 173.338029
> vlimit exceeded for step 11; vmax = 434.991607
> vlimit exceeded for step 12; vmax = 147.34334
> vlimit exceeded for step 13; vmax = 80.8046939
> vlimit exceeded for step 14; vmax = 80.5587922
> vlimit exceeded for step 15; vmax = 1471.60039
> vlimit exceeded for step 16; vmax = 80.0696426
> vlimit exceeded for step 17; vmax = 79.8330323
> vlimit exceeded for step 18; vmax = 79.6017966
> vlimit exceeded for step 19; vmax = 79.3746615
> vlimit exceeded for step 20; vmax = 79.1385957
> vlimit exceeded for step 21; vmax = 78.8850897
> vlimit exceeded for step 22; vmax = 78.5758855
> vlimit exceeded for step 23; vmax = 78.2741297
> vlimit exceeded for step 24; vmax = 77.9481826
> vlimit exceeded for step 25; vmax = 85.172779
> vlimit exceeded for step 26; vmax = 77.2745741
> vlimit exceeded for step 27; vmax = 76.9446935
> vlimit exceeded for step 28; vmax = 76.627078
> vlimit exceeded for step 29; vmax = 3397.81899
> vlimit exceeded for step 30; vmax = 76.0964907
> vlimit exceeded for step 31; vmax = 75.9137909
> vlimit exceeded for step 32; vmax = 75.8097905
> vlimit exceeded for step 33; vmax = 75.7734782
> vlimit exceeded for step 34; vmax = 75.7649366
> vlimit exceeded for step 35; vmax = 75.7567528
> vlimit exceeded for step 36; vmax = 75.7495732
> vlimit exceeded for step 37; vmax = 75.7434868
> vlimit exceeded for step 38; vmax = 73488.7837
> vlimit exceeded for step 39; vmax = 75.7328433
> vlimit exceeded for step 40; vmax = 75.7284959
> vlimit exceeded for step 41; vmax = 75.7245491
> vlimit exceeded for step 42; vmax = 775.454355
> vlimit exceeded for step 43; vmax = 75.7162903
> vlimit exceeded for step 44; vmax = 75.711727
> vlimit exceeded for step 45; vmax = 75.7068749
> vlimit exceeded for step 46; vmax = 75.7020602
> vlimit exceeded for step 47; vmax = 75.6975821
> vlimit exceeded for step 48; vmax = 75.6935556
> vlimit exceeded for step 49; vmax = 75.6901533
>
> NSTEP = 50 TIME(PS) = 0.050 TEMP(K) = nan PRESS = 0.0
> Etot = nan EKtot = nan EPtot = nan
> BOND = 193318.0575 ANGLE = nan DIHED = 116.9248
> 1-4 NB = 2425.1376 1-4 EEL = 420.0159 VDWAALS = 8453.2431
> EELEC = -170.1844 EHBOND = 0.0000 RESTRAINT = 0.0000
> ------------------------------------------------------------------------------
>
> vlimit exceeded for step 50; vmax = 83.3956481
> vlimit exceeded for step 51; vmax = 75.6851903
> vlimit exceeded for step 52; vmax = 75.6834912
> vlimit exceeded for step 53; vmax = 75.6818567
> vlimit exceeded for step 54; vmax = 160.110583
> vlimit exceeded for step 55; vmax = 75.6798846
> vlimit exceeded for step 56; vmax = 75.6798899
> vlimit exceeded for step 57; vmax = 413.502874
> vlimit exceeded for step 58; vmax = 282.051973
> vlimit exceeded for step 59; vmax = 75.679949
> vlimit exceeded for step 60; vmax = 75.6799745
> vlimit exceeded for step 61; vmax = 75.6800103
> vlimit exceeded for step 62; vmax = 76.451566
> vlimit exceeded for step 63; vmax = 75.680118
> vlimit exceeded for step 64; vmax = 75.6801905
> vlimit exceeded for step 65; vmax = 75.6802722
> vlimit exceeded for step 66; vmax = 99.9119017
> vlimit exceeded for step 67; vmax = 107.599584
> vlimit exceeded for step 68; vmax = 75.680529
> vlimit exceeded for step 69; vmax = 75.6806056
> vlimit exceeded for step 70; vmax = 75.6806739
> vlimit exceeded for step 71; vmax = 75.6807332
> vlimit exceeded for step 72; vmax = 75.6807842
> vlimit exceeded for step 73; vmax = 2198.5185
> vlimit exceeded for step 74; vmax = 75.680913
> vlimit exceeded for step 75; vmax = 75.6810012
> vlimit exceeded for step 76; vmax = 75.6811096
> vlimit exceeded for step 77; vmax = 75.6812408
> vlimit exceeded for step 78; vmax = 114.163678
> vlimit exceeded for step 79; vmax = 75.6815795
> vlimit exceeded for step 80; vmax = 75.6627231
> Frac coord min, max: -0.00356895655 0.680901547
> The system has extended beyond
> the extent of the virtual box.
> Restarting sander will recalculate
> a new virtual box with 30 Angstroms
> extra on each side, if there is a
> restart file for this configuration.
> EWALD BOMB in subroutine Routine: map_coords (ew_force.f)
> Atom out of bounds. If a restart has been written,
> restarting should resolve the error
>
>
>
>
> I do what the program asks and use the "-c restrt" option in sander and
> change "NTX=5" and "IREST=1" in md0.in file, and it keeps falling in the
> same errors until the output turns to be:
>
>
>
>
> -------------------------------------------------------
> Amber 7 SANDER Scripps/UCSF 2002
> -------------------------------------------------------
>
> | Tue Jul 29 15:17:29 2003
>
> [-O]verwriting output
>
> File Assignments:
> | MDIN:
> md0.in
> | MDOUT:
> md0.out
> |INPCRD:
> restrt
> | PARM:
> alphacd.top
> |RESTRT:
> restrt
> | REFC:
> refc
> | MDVEL:
> md0.vel
> | MDEN:
> md0.en
> | MDCRD:
> md0.crd
> |MDINFO:
> mdinfo
> |INPDIP:
> inpdip
> |RSTDIP:
> rstdip
>
>
> Here is the input file:
>
> # IMIN -> tipo de
> simulacao
> # NTX, IREST -> nature and format of
> input
> # NTWX, NTWV, NTWE, NTWR, NTPR -> nature ando format of
> output
> # NTB -> Periodic
> boundary
> # NSTLIM, NSCM -> MD run
> flags
> # NTT, TEMP0, TAUTP -> Temperature
> regulation
> # NTC ->
> Shake
>
>
> alpha-ciclodextrina isolada a temperatura ambiente
> (equilibracao)
> &cntrl
>
> IMIN=0, IREST=1,
> NTX=5,
> NTWX=50, NTWV=50,
> NTWR=50,
> NTWE=50,
> NTPR=50,
>
> NSTLIM=5000,
> NTB=0,
> NSCM=100,
>
> NTC=1,
> NTT=1, TEMP0=298.15,
> TAUTP=1.0,
> &end
>
>
>
>
>
>
> --------------------------------------------------------------------------------
> 1. RESOURCE USE:
> --------------------------------------------------------------------------------
>
> |
> Flags:
>
> | NONPERIODIC ntb=0 and igb=0: Setting up nonperiodic simulation
> | New format PARM file being parsed.
> | Version = 1.000 Date = 06/17/03 Time = 17:07:40
> NATOM = 126 NTYPES = 6 NBONH = 60 MBONA = 65
> NTHETH = 134 MTHETA = 90 NPHIH = 287 MPHIA = 192
> NHPARM = 0 NPARM = 0 NNB = 661 NRES = 1
> NBONA = 65 NTHETA = 90 NPHIA = 192 NUMBND = 6
> NUMANG = 11 NPTRA = 12 NATYP = 6 NPHB = 0
> IFBOX = 0 NMXRS = 126 IFCAP = 0 NEXTRA = 0
>
>
> Static Integer Memory requirement of: 2412704 exceeds MAXINT of
> 2000000
>
> | Memory Use Allocated Used
> | Real 2000000 10412
> | Hollerith 400000 759
> | Integer 2000000 2412704
>
> | Max Nonbonded Pairs: 5400000
> ** Redimension and recompile
>
>
>
>
> What is wrong?? I'd appreciate any help....
> Thanks in advance,
> Herbert
>
>
> -----------------------------------------------------------------------
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