Hi Subramanian,
Unfortunately your mail client destroyed the formatting of your output
file which makes it very difficult to read. It would help if you can
repost it as an attachment. It would also be useful to know the steps you
took prior to running the MD here. Did you minimize your system? What did
the structure look like after minimization? Normally limit errors are
caused by atoms sitting on top of each other which give very large VDW
energies and forces but this is not obvious from your output here. My
suggestion would be to run the calculation again but set nstlim=100,
ntpr=1, ntwx=1. This will give you a trajectory frame on every step which
you can then visualize in VMD. From there it should be possible to see
specifically which atom it is that is exceeding the limit and this should
provide you a clue to what is wrong with your initial structure.
All the best
Ross
On 11/1/12 9:55 PM, "subramanian boopathi" <boopathialzheimer.hotmail.com>
wrote:
>
>
>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 - 23:00:03 PDT
