hello,
what is box size u started with.
I am not sure but it might due to have overlapping atoms (in periodic
image), and the van der waals clash is supplying a
repulsive force significantly large to induce such large velocities
regards
vinod
On Wed, Mar 31, 2010 at 9:34 AM, Nicee <nicee.srivastava.imtech.res.in>wrote:
> Thank you for your reply sir. As the reference structure i am using the
> initial
> structure in the inpcrd file.
>
> The output file for the step 2 is below:
>
> File Assignments:
> | MDIN: md2.in
> | MDOUT: model_noref_3g5a_md2.out
> |INPCRD: model_noref_3g5a_md1.restrt
> | PARM: model_noref_3g5a.prmtop
> |RESTRT: model_noref_3g5a_md2.restrt
> | REFC: model_noref_3g5a.inpcrd
> | MDVEL: mdvel
> | MDEN: mden
> | MDCRD: model_noref_3g5a_md2.mdcrd
> |MDINFO: mdinfo
> |INPDIP: inpdip
> |RSTDIP: rstdip
>
>
> Here is the input file:
>
> Equilibration 2 with decreasing restraint on protein and constraint on
> hydrogen
> &cntrl
> imin = 0, ntb = 1,
> igb = 0, ntpr = 2000, ntwx = 2000,
> iwrap=1,
> irest=1, ntx=5,
> ntt = 3, gamma_ln = 1.0,
> tempi=300, temp0=300,
> ntc=2, ntf=2
> ntr=1,
> nstlim = 200000, dt = 0.002,
> cut = 12
> /
> HOLD THE PROTEIN FIXED
> 2.5
> RES 1 306
> END
> END
>
>
> --------------------------------------------------------------------------------
> 1. RESOURCE USE:
>
> --------------------------------------------------------------------------------
>
> | Flags: MPI
> getting new box info from bottom of inpcrd
> | INFO: Old style inpcrd file read
>
> | peek_ewald_inpcrd: Box info found
> |Largest sphere to fit in unit cell has radius = 34.331
> | New format PARM file being parsed.
> | Version = 1.000 Date = 03/16/10 Time = 22:34:34
> NATOM = 40391 NTYPES = 17 NBONH = 37867 MBONA = 2583 NTHETH
> =
> 5493 MTHETA = 3505 NPHIH = 10625 MPHIA = 8674 NHPARM = 0
> NPARM
> = 0 NNB = 74540 NRES = 12133 NBONA = 2583 NTHETA =
> 3505
> NPHIA = 8674 NUMBND = 43 NUMANG = 89 NPTRA = 42 NATYP =
> 31 NPHB = 1 IFBOX = 2 NMXRS = 24 IFCAP = 0
> NEXTRA =
> 0 NCOPY = 0
>
>
> | Memory Use Allocated
> | Real 2305112
> | Hollerith 254481
> | Integer 1265458
> | Max Pairs 3078691
> | nblistReal 484692
> | nblist Int 1179046
> | Total 44364 kbytes
> | Duplicated 0 dihedrals
> | Duplicated 0 dihedrals
>
> BOX TYPE: TRUNCATED OCTAHEDRON
> 2. CONTROL DATA FOR THE RUN
>
> --------------------------------------------------------------------------------
>
>
>
> General flags:
> imin = 0, nmropt = 0
>
> Nature and format of input:
> ntx = 5, irest = 1, ntrx = 1
>
> Nature and format of output:
> ntxo = 1, ntpr = 2000, ntrx = 1, ntwr =
> 500
> iwrap = 1, ntwx = 2000, 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 = 12.00000, intdiel = 1.00000 scnb =
> 2.00000, scee = 1.20000
>
> Frozen or restrained atoms:
> ibelly = 0, ntr = 1
>
> Molecular dynamics:
> nstlim = 200000, nscm = 1000, nrespa = 1 t =
> 0.00000, dt = 0.00200, vlimit = 20.00000
>
> Langevin dynamics temperature regulation:
> ig = 71277
> temp0 = 300.00000, tempi = 300.00000, 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 = 84.093 Box Y = 84.093 Box Z = 84.093
> Alpha = 109.471 Beta = 109.471 Gamma = 109.471
> NFFT1 = 90 NFFT2 = 90 NFFT3 = 90
> Cutoff= 12.000 Tol =0.100E-04
> Ewald Coefficient = 0.22664
> Interpolation order = 4
> | MPI Timing options:
> | profile_mpi = 0
>
> LOADING THE CONSTRAINED ATOMS AS GROUPS
>
>
> 5. REFERENCE ATOM COORDINATES
>
>
> ----- READING GROUP 1; TITLE:
> HOLD THE PROTEIN FIXED
>
> GROUP 1 HAS HARMONIC CONSTRAINTS 2.50000
> GRP 1 RES 1 TO 306
> Number of atoms in this group = 4932
> ----- END OF GROUP READ -----
>
>
> --------------------------------------------------------------------------------
> 3. ATOMIC COORDINATES AND VELOCITIES
>
> --------------------------------------------------------------------------------
> begin time read from input coords = 1200.000 ps
> Number of triangulated 3-point waters found: 11816
> | Atom division among processors:
> | 0 2533 5048 7574 10097 12620 15146 17669 |
> 20192
> 22718 25241 27764 30290 32813 35336 37862 | 40391
>
> Sum of charges from parm topology file = -0.00000015
> Forcing neutrality...
> | Running AMBER/MPI version on 16 nodes
>
>
>
> --------------------------------------------------------------------------------
> 4. RESULTS
>
> --------------------------------------------------------------------------------
>
> | # of SOLUTE degrees of freedom (RNDFP): 83306.
> | # of SOLVENT degrees of freedom (RNDFS): 0.
> | NDFMIN = 83306. NUM_NOSHAKE = 0 CORRECTED RNDFP =
> 83306. |
> TOTAL # of degrees of freedom (RNDF) = 83306.
> ---------------------------------------------------
> 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 = 0.2738E-14 at 2.422500
> | CHECK d/dx switch(x): max rel err = 0.7967E-11 at 2.716640
> ---------------------------------------------------
> | Local SIZE OF NONBOND LIST = 1235560
> | TOTAL SIZE OF NONBOND LIST = 21674999
> vlimit exceeded for step 1; vmax = 31.5574
>
> Coordinate resetting (SHAKE) cannot be accomplished,
> deviation is too large
> NITER, NIT, LL, I and J are : 0 2 489 980 981
>
>
> kindly help and suggest.
>
> Thanking you.
>
> Nicee
>
>
> > your initial restraint energies are very large- i suspect you are not
> using
> the correct reference structure.
> > hard to say what's wrong with step 2 since you didn't provide the output.
> >
> > On Tue, Mar 30, 2010 at 12:37 AM, Nicee <nicee.srivastava.imtech.res.in
> >wrote:
> >
> >> Hello,
> >>
> >> I m running a simulation of a protein model with Amber10 and during
> second step
> >> of equilibration im getting following error.
> >>
> >> vlimit exceeded for step 1; vmax = 31.5574
> >>
> >> Coordinate resetting (SHAKE) cannot be accomplished,
> >> deviation is too large
> >> NITER, NIT, LL, I and J are : 0 2 489 980 981
> >>
> >> Note: This is usually a symptom of some deeper
> >> problem with the energetics of the system.
> >>
> >> Earlier i had minimized the protein for 500 steps. Then heated it
> gradually
> during first equilibration at nvt with shake on hydrogen bonds and restrain
> on
> >> protein with a force constant of 5kcal/mol A. Im attaching the input and
> output
> >> file of this first equilibration.
> >> Input for the first equilibration is:
> >>
> >> Equilibration 1 with restraint on protein and constraint on hydrogen
> bonds
> >> &cntrl
> >> imin = 0, ntb = 1,
> >> igb = 0, ntpr = 2000, ntwx = 2000,
> >> iwrap=1,
> >> ntt = 3, gamma_ln = 1.0,
> >> tempi = 0,
> >> ntc=2, ntf=2,
> >> ntr=1, nmropt=1,
> >> nstlim = 600000, dt = 0.002,
> >> cut = 12.0
> >>
> >> &end
> >> &wt
> >> type='TEMP0', istep1=0, istep2=20000,
> >> value1=0, value2=10,
> >> &end
> >> &wt
> >> type='TEMP0', istep1=20001, istep2=40000,
> >> value1=11, value2=20,
> >> &end
> >> &wt
> >> type='TEMP0', istep1=40001, istep2=60000,
> >> value1=21, value2=30,
> >> &end
> >> &wt
> >> type='TEMP0', istep1=60001, istep2=80000,
> >> value1=31, value2=40,
> >> &end
> >> &wt
> >> type='TEMP0', istep1=80001, istep2=100000,
> >> value1=41, value2=50,
> >> &end
> >> &wt
> >> type='TEMP0', istep1=100001, istep2=120000,
> >> value1=51, value2=60,
> >> &end
> >> &wt
> >> type='TEMP0', istep1=120001, istep2=140000,
> >> value1=61, value2=70,
> >> &end
> >> &wt
> >> type='TEMP0', istep1=140001, istep2=160000,
> >> value1=71, value2=80,
> >> &end
> >> &wt
> >> type='TEMP0', istep1=160001, istep2=180000,
> >> value1=81, value2=90,
> >> &end
> >> &wt
> >> type='TEMP0', istep1=180001, istep2=200000,
> >> value1=91, value2=100,
> >> &end
> >> &wt
> >> type='TEMP0', istep1=200001, istep2=220000,
> >> value1=101, value2=110,
> >> &end
> >> &wt
> >> type='TEMP0', istep1=220001, istep2=240000,
> >> value1=111, value2=120,
> >> &end
> >> &wt
> >> type='TEMP0', istep1=240001, istep2=260000,
> >> value1=121, value2=130,
> >> &end
> >> &wt
> >> type='TEMP0', istep1=260001, istep2=280000,
> >> value1=131, value2=140,
> >> &end
> >> &wt
> >> type='TEMP0', istep1=280001, istep2=300000,
> >> value1=141, value2=150,
> >> &end
> >> &wt
> >> type='TEMP0', istep1=300001, istep2=320000,
> >> value1=151, value2=160
> >> &end
> >> &wt
> >> type='TEMP0', istep1=320001, istep2=340000,
> >> value1=161, value2=170
> >> &end
> >> &wt
> >> type='TEMP0', istep1=340001, istep2=360000,
> >> value1=171, value2=180,
> >> &end
> >> &wt
> >> type='TEMP0', istep1=360001, istep2=380000,
> >> value1=181, value2=190,
> >> &end
> >> &wt
> >> type='TEMP0', istep1=380001, istep2=400000,
> >> value1=191, value2=200,
> >> &end
> >> &wt
> >> type='TEMP0', istep1=400001, istep2=420000,
> >> value1=201, value2=210,
> >> &end
> >> &wt
> >> type='TEMP0', istep1=420001, istep2=440000,
> >> value1=211, value2=220
> >> &end
> >> &wt
> >> type='TEMP0', istep1=440001, istep2=460000,
> >> value1=221, value2=230,
> >> &end
> >> &wt
> >> type='TEMP0', istep1=460001, istep2=480000,
> >> value1=231, value2=240,
> >> &end
> >> &wt
> >> type='TEMP0', istep1=480001, istep2=500000,
> >> value1=241, value2=250,
> >> &end
> >> &wt
> >> type='TEMP0', istep1=500001, istep2=520000,
> >> value1=251, value2=260,
> >> &end
> >> &wt
> >> type='TEMP0', istep1=520001, istep2=540000,
> >> value1=261, value2=270
> >> &end
> >> &wt
> >> type='TEMP0', istep1=540001, istep2=560000,
> >> value1=271, value2=280,
> >> &end
> >> &wt
> >> type='TEMP0', istep1=560001, istep2=580000,
> >> value1=281, value2=290,
> >> &end
> >> &wt
> >> type='TEMP0', istep1=580001, istep2=600000,
> >> value1=291, value2=300,
> >> &end
> >> &wt
> >> type='END'
> >> /
> >> HOLD THE PROTEIN FIXED
> >> 5.0
> >> RES 1 306
> >> END
> >> END
> >>
> >> It went fine. Next i wanted to decrease the force constant gradually
> keeping the
> >> temperature constant. I had planed out different equilibration steps
> with
> decreasing the force constant to 2.5, 1.0, 0.0 for every 200000
> steps,keeping
> >> temperature constant, nvt ensemble, and shake constrain on hydrogen
> bonds. But
> >> the second equilibration didnt even started and ended up with the above
> error.
> >>
> >> The input file for second equilibration is:
> >>
> >> Equilibration 2 with decreasing restraint on protein and constraint on
> hydrogen
> >> bonds
> >> &cntrl
> >> imin = 0, ntb = 1,
> >> igb = 0, ntpr = 2000, ntwx = 2000,
> >> iwrap=1,
> >> irest=1,ntx=5,
> >> ntt = 3, gamma_ln = 1.0,
> >> tempi = 300, temp0=300,
> >> ntc=2, ntf=2,
> >> ntr=1,
> >> nstlim = 200000, dt = 0.002,
> >> cut = 12
> >> /
> >> HOLD THE PROTEIN FIXED
> >> 2.5
> >> RES 1 306
> >> END
> >> END
> >>
> >> Does this problem has anything to do with shake, should i not use it. Or
> does it
> >> has anything to do with ntt=3, should i use berendsen method with ntt=1(
> Im
> really confused with this ).Is this way of giving restraint is fine or
> should
> i
> >> use resatrain_mask and restarin_wt. Can the problem be due to the cut
> off,
> should I decrease it. Kindly help with the problem n suggest something.
> >>
> >> One more thing, on visualizing the protein after first equilibration on
> VMD it
> >> was observed that protein was coming out of the water box starting from
> the
> first step.However, it was well within the water box at the end of
> minimization.
> >> How and why did this happened. Kindly explain.
> >>
> >> Thanking you.
> >>
> >> Nicee.
> >>
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >>
> >
>
>
>
>
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Received on Wed Mar 31 2010 - 00:30:02 PDT
