Try temp0=100. Less violent warming from 0.
Bill
subramanian boopathi <boopathialzheimer.hotmail.com> wrote:
>
> dear sir
> My structure contain small fragment of protein with drug molecules, which contains 114 atoms. i have successfully run two energy minimization process. unfortunately in case of heating process i have face vlimit exceeded error, i am not able rectify after multiple approaches, My input file is below
>
>
> Molecular Dynamics(heating)(20ps MD) with restraints on solute
> &cntrl
> imin = 0,
> irest = 0,
> ntx = 1,
> ntb = 1,
> cut = 15.0,
> ntr = 1,
> 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 88
> RES 89 114
> END
> END
>
> Initially i have set box size (18*18*18*) 5834 squab of angstrom when i gave input file as cut=8.0 angstrom. unfortunetly vlimit exceeded error for step 1.
> secondly i have changed ntt=1 as for ntt=3,
> Restrain also increase upto 500kcal/mol
> i have fixed the constant temprature that is ntb=2, ntp =1 option used
> finally time option reduced as dt= 0.0002 option choose
> but fragment of protein without dug has been successfullly run upto production, in the case addition add the drug with the fragment of protein when i am facing v limit exceeded error for step 1
> the above all tries not succeed to overcome vlimit exceeded error. could you please give suggestion for what i made a mistake and to overcome this problem
>
> my output file shown below
>
>
> -------------------------------------------------------
> Amber 8 SANDER Scripps/UCSF 2004
> -------------------------------------------------------
>
> | Run on 05/17/1998 at 23:29:15
> [-O]verwriting output
>
> File Assignments:
> | MDIN: ab17-21md1.in
> | MDOUT: ab17-21md1.out
> |INPCRD: ab17-21min2.rst
> | PARM: ab17-21wat.top
> |RESTRT: ab17-21md1.rst
> | REFC: ab17-21min2.rst
> | MDVEL: mdvel
> | MDEN: mden
> | MDCRD: ab17-21md1.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 = 15.0,
> ntr = 1,
> 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 88
> RES 89 114
> 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 = 38.538
> | New format PARM file being parsed.
> | Version = 1.000 Date = 05/17/98 Time = 17:42:13
> NATOM = 40800 NTYPES = 13 NBONH = 40745 MBONA = 57
> NTHETH = 130 MTHETA = 76 NPHIH = 223 MPHIA = 130
> NHPARM = 0 NPARM = 0 NNB = 54869 NRES = 13563
> NBONA = 57 NTHETA = 76 NPHIA = 130 NUMBND = 19
> NUMANG = 36 NPTRA = 28 NATYP = 16 NPHB = 1
> IFBOX = 1 NMXRS = 114 IFCAP = 0 NEXTRA = 0
> NCOPY = 0
>
>
> | Memory Use Allocated
> | Real 2918977
> | Hollerith 258365
> | Integer 2047399
> | Max Pairs 66816800
> | Max Rstack 2368794
> | Max Istack 204000
> | Total 312117 kbytes
> | Duplicated 0 dihedrals
> | Duplicated 0 dihedrals
>
> BOX TYPE: RECTILINEAR
>
> --------------------------------------------------------------------------------
> 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 = 15.00000, 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 = 81.325 Box Y = 77.891 Box Z = 77.076
> Alpha = 90.000 Beta = 90.000 Gamma = 90.000
> NFFT1 = 90 NFFT2 = 80 NFFT3 = 80
> Cutoff= 15.000 Tol =0.100E-04
> Ewald Coefficient = 0.17871
> 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 88
> GRP 1 RES 89 TO 114
> Number of atoms in this group = 453
> ----- 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: 13562
>
> 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 = 0.7799E-11 at 2.634640
> ---------------------------------------------------
> | Local SIZE OF NONBOND LIST = 36119819
> | TOTAL SIZE OF NONBOND LIST = 36119819
>
> NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS = 0.0
> Etot = -184524.8822 EKtot = 0.0000 EPtot = -184524.8822
> BOND = 2.7438 ANGLE = 10.0944 DIHED = 37.0235
> 1-4 NB = 27.9204 1-4 EEL = 0.0000 VDWAALS = 37748.3493
> EELEC = -222351.0136 EHBOND = 0.0000 RESTRAINT = 0.0000
> Ewald error estimate: 0.2592E-03
> ------------------------------------------------------------------------------
>
> vlimit exceeded for step 1 ; vmax = 27.120046866612064
>
>
>
>
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Received on Tue Nov 27 2012 - 23:30:03 PST
