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.
>>
>>
>> _______________________________________________
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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>
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Received on Tue Mar 30 2010 - 05:00:03 PDT
