dear user
help me to overcome the following vlimit error and my structure contain 130 residues of oligopeptide with 27 residue of molecules.
------------------------------------------------------- Amber 8 SANDER Scripps/UCSF 2004 -------------------------------------------------------
| Run on 05/19/1998 at 20:24:04 [-O]verwriting output
File Assignments:| MDIN: abnicmd1.in | MDOUT: abnicmd1.out |INPCRD: abnicmin2.rst | PARM: abnicwat.top |RESTRT: abnicmd1.rst | REFC: abnicmin2.rst | MDVEL: mdvel | MDEN: mden | MDCRD: abnicmd1.mdcrd |MDINFO: mdinfo |INPDIP: inpdip |RSTDIP: rstdip
Here is the input file: Molecular Dynamics(heating)(20ps MD) with restraints on solute &cntrl imin = 0, irest = 0, ntx = 1, ntb = 1, cut = 8.0, ntr = 1, ntc = 2, ntf = 2, tempi = 0.0, temp0 = 300.0, ntt = 3,
gamma_ln = 1.0, nstlim = 10000, dt = 0.002 ntpr = 100, ntwx = 100, ntwr = 1000 / Keep the solute fixed with weak restraints 10.0 RES 1 157 END END
-------------------------------------------------------------------------------- 1. RESOURCE USE: --------------------------------------------------------------------------------
| Flags: SGIFFT getting new box info from bottom of inpcrd| peek_ewald_inpcrd: Box info found|Largest sphere to fit in unit cell has radius = 13.734| New format PARM file being parsed.| Version = 1.000 Date = 05/19/98 Time = 19:30:48 NATOM = 2311 NTYPES = 13 NBONH = 2235 MBONA = 78 NTHETH = 181 MTHETA = 103 NPHIH = 321 MPHIA = 181 NHPARM = 0 NPARM = 0 NNB = 3726 NRES = 719 NBONA = 78 NTHETA = 103 NPHIA = 181 NUMBND = 19 NUMANG = 37 NPTRA = 28 NATYP = 16 NPHB = 1 IFBOX = 2 NMXRS = 157 IFCAP = 0 NEXTRA = 0 NCOPY = 0
| Memory Use Allocated| Real 245932| Hollerith 14587| Integer 184235| Max Pairs 770333| Max Rstack 172964| Max Istack 11555| Total 7103 kbytes| Duplicated 0 dihedrals| Duplicated 0 dihedrals
BOX TYPE: TRUNCATED OCTAHEDRON
-------------------------------------------------------------------------------- 2. CONTROL DATA FOR THE RUN--------------------------------------------------------------------------------
MOL
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 = 100, ntrx = 1, ntwr = 1000 iwrap = 0, ntwx = 100, ntwv = 0, ntwe = 0 ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0
Potential function: ntf = 2, ntb = 1, igb = 0, nsnb = 25 ipol = 0, gbsa = 0, iesp = 0 dielc = 1.00000, cut = 8.00000, intdiel = 1.00000 scnb = 2.00000, scee = 1.20000
Frozen or restrained atoms: ibelly = 0, ntr = 1
Molecular dynamics: nstlim = 10000, nscm = 1000, nrespa = 1 t = 0.00000, dt = 0.00200, vlimit = 20.00000
Langevin dynamics temperature regulation: ig = 71277 temp0 = 300.00000, tempi = 0.00000, gamma_ln= 1.00000
SHAKE: ntc = 2, jfastw = 0 tol = 0.00001
Ewald parameters: verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1 vdwmeth = 1, eedmeth = 1, netfrc = 1 Box X = 33.640 Box Y = 33.640 Box Z = 33.640 Alpha = 109.471 Beta = 109.471 Gamma = 109.471 NFFT1 = 36 NFFT2 = 36 NFFT3 = 36 Cutoff= 8.000 Tol =0.100E-04 Ewald Coefficient = 0.34864 Interpolation order = 4
LOADING THE CONSTRAINED ATOMS AS GROUPS
5. REFERENCE ATOM COORDINATES
MOL ----- READING GROUP 1; TITLE: Keep the solute fixed with weak restraints
GROUP 1 HAS HARMONIC CONSTRAINTS 10.00000 GRP 1 RES 1 TO 157 Number of atoms in this group = 625 ----- END OF GROUP READ -----
-------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES--------------------------------------------------------------------------------
MOL begin time read from input coords = 0.000 ps
Number of triangulated 3-point waters found: 718
Sum of charges from parm topology file = 0.00000000 Forcing neutrality...
-------------------------------------------------------------------------------- 4. RESULTS--------------------------------------------------------------------------------
--------------------------------------------------- APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION using 5000.0 points per unit in tabled values TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff| CHECK switch(x): max rel err = 0.2890E-14 at 2.422500| CHECK d/dx switch(x): max rel err = 0.8329E-11 at 2.782960 ---------------------------------------------------| Local SIZE OF NONBOND LIST = 377374| TOTAL SIZE OF NONBOND LIST = 377374
NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS = 0.0 Etot = -9341.2417 EKtot = 0.0000 EPtot = -9341.2417 BOND = 3.2349 ANGLE = 20.9786 DIHED = 101.7711 1-4 NB = 32.0698 1-4 EEL = 0.0000 VDWAALS = 1736.8722 EELEC = -11236.1683 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.2714E-03 ------------------------------------------------------------------------------
vlimit exceeded for step 1 ; vmax = 120.59491482799595
NSTEP = 100 TIME(PS) = 0.200 TEMP(K) = NaN PRESS = 0.0 Etot = NaN EKtot = NaN EPtot = NaN BOND = 3.3768 ANGLE = 21.0263 DIHED = 101.6906 1-4 NB = 32.0295 1-4 EEL = 0.0000 VDWAALS = 2017.6777 EELEC = NaN EHBOND = 0.0000 RESTRAINT = 118101856.8005 EAMBER (non-restraint) = NaN Ewald error estimate: NaN ------------------------------------------------------------------------------
NSTEP = 200 TIME(PS) = 0.400 TEMP(K) = NaN PRESS = 0.0 Etot = NaN EKtot = NaN EPtot = NaN BOND = 3.3768 ANGLE = 21.0263 DIHED = 101.6906 1-4 NB = 32.0295 1-4 EEL = 0.0000 VDWAALS = 1741.7027 EELEC = NaN EHBOND = 0.0000 RESTRAINT = 487134893.1609 EAMBER (non-restraint) = NaN Ewald error estimate: NaN ------------------------------------------------------------------------------
NSTEP = 300 TIME(PS) = 0.600 TEMP(K) = NaN PRESS = 0.0 Etot = NaN EKtot = NaN EPtot = NaN BOND = 3.3768 ANGLE = 21.0263 DIHED = 101.6906 1-4 NB = 32.0295 1-4 EEL = 0.0000 VDWAALS = 2024.0824 EELEC = NaN EHBOND = 0.0000 RESTRAINT = ************** EAMBER (non-restraint) = NaN Ewald error estimate: NaN ------------------------------------------------------------------------------
NSTEP = 400 TIME(PS) = 0.800 TEMP(K) = NaN PRESS = 0.0 Etot = NaN EKtot = NaN EPtot = NaN BOND = 3.3768 ANGLE = 21.0263 DIHED = 101.6906 1-4 NB = 32.0295 1-4 EEL = 0.0000 VDWAALS = 2023.9384 EELEC = NaN EHBOND = 0.0000 RESTRAINT = ************** EAMBER (non-restraint) = NaN Ewald error estimate: NaN ------------------------------------------------------------------------------
NSTEP = 500 TIME(PS) = 1.000 TEMP(K) = NaN PRESS = 0.0 Etot = NaN EKtot = NaN EPtot = NaN BOND = 3.3768 ANGLE = 21.0263 DIHED = 101.6906 1-4 NB = 32.0295 1-4 EEL = 0.0000 VDWAALS = 2025.5741 EELEC = NaN EHBOND = 0.0000 RESTRAINT = ************** EAMBER (non-restraint) = NaN Ewald error estimate: NaN ------------------------------------------------------------------------------
NSTEP = 600 TIME(PS) = 1.200 TEMP(K) = NaN PRESS = 0.0 Etot = NaN EKtot = NaN EPtot = NaN BOND = 3.3768 ANGLE = 21.0263 DIHED = 101.6906 1-4 NB = 32.0295 1-4 EEL = 0.0000 VDWAALS = NaN EELEC = NaN EHBOND = 0.0000 RESTRAINT = ************** EAMBER (non-restraint) = NaN Ewald error estimate: NaN ------------------------------------------------------------------------------
NSTEP = 700 TIME(PS) = 1.400 TEMP(K) = NaN PRESS = 0.0 Etot = NaN EKtot = NaN EPtot = NaN BOND = 3.3768 ANGLE = 21.0263 DIHED = 101.6906 1-4 NB = 32.0295 1-4 EEL = 0.0000 VDWAALS = 1851.7520 EELEC = NaN EHBOND = 0.0000 RESTRAINT = ************** EAMBER (non-restraint) = NaN Ewald error estimate: NaN ------------------------------------------------------------------------------
and my frcmod file is
remark goes hereMASS
BOND
ANGLEca-c3-n3 66.152 111.475 Calculated with empirical approach
DIHE
IMPROPER
NONBON
with regards
S. Boopathi
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Received on Thu Nov 01 2012 - 22:00:03 PDT
