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
>> >>
>> >>
>> >
>>
>>
>>
>>
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Received on Wed Mar 31 2010 - 00:30:03 PDT
