no you should not need to change the box size.
what concerns me is the messages in the md1 output of "wrapping first mol.".
it doesn't seem that the first molecule should be wrapped if it has
positional restraints, unless your refc has it very close to the box edge.
maybe it would help to do graphical visualization of the md1 trajectory and
see what is happening.
On Wed, Mar 31, 2010 at 3:26 AM, Nicee <nicee.srivastava.imtech.res.in>wrote:
> Thank you for the reply sir. The water box i started with was octahedral
> box
> with minimum distance of 8 A. Should i decrease the cut off value.
>
> Thanking you.
> Nicee.
>
>
> > 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
> >> >>
> >> >>
> >> >
> >>
> >>
> >>
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
>
>
> _______________________________________________
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Received on Wed Mar 31 2010 - 04:30:03 PDT
