AMBER Archive (2003)

Subject: Re: AMBER: dynamics of isolated system

From: Herbert Georg (hcgeorg_at_if.usp.br)
Date: Tue Jul 29 2003 - 14:05:45 CDT

Well,

That is what it looks to me too...
But let's go to the information... The system is isolated, so it's just
one molecule alone, without solvent, that's why I used ntb=0. The
molecule is alpha-cyclodextrin and I got the geometry from an MM
optimization using AMBER94 parm.
I'm just trying to perform the equilibration. Do I have to do something
different in equilibration runs/steps, maybe some additional variable
settings??
What value for NTT would be good for such a run, considering that I
would like to simulate the system alone at room temperature??

Thanks again,
Herbert

Vlad Cojocaru escreveu:

> This looks like you just put something and it blew up. NOW:
> What system do you have: is it solvated? (if not using ntt=1 makes not
> to much sense)
> Did you equilibrated it before running this? (this looks to me very
> cruel to the system..maybe you can consider an equilibration step
> before)..
> But an answer makes no sense I think before you tell us what system do
> you have there . From ntb=0 i thought it is not an explicit solvent
> simulation...
> How did you get your initial structure?
> And so on..
> Vlad
>
> 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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>

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