Hi Daniel,
I am running minimization in three steps, with PBC on,
1. all atoms restrained
2. only protein backbone atoms restrained
3. all atoms free
all with 2500 steepest descent and 5000 conjugate gradient steps.
and then moving to run heating and equilibration with following input
Initial heating and equilabration
&cntrl
imin=0, irest=0, ntx=1,ig=-1,
nstlim=100000, dt=0.001,
ntpr=100, ntwx=10,
ntr=1, restraintmask=':1-356',
restraint_wt=1.0,
cut=16.0, ntb=1, ntc=2, ntf=2,
ntt=3, gamma_ln=1.0,
tempi=0.0, temp0=300.0,
/
still the run persists with same vlimit exceeded error. output is;
-------------------------------------------------------
Amber 11 SANDER 2010
-------------------------------------------------------
| Run on 10/10/2012 at 15:01:09
[-O]verwriting output
File Assignments:
| MDIN: complex-equi.in
| MDOUT: complex-equi.out
|INPCRD: complex-min3.rst
| PARM: complex-water.top
|RESTRT: complex-equi.rst
| REFC: complex-min3.rst
| MDVEL: mdvel
| MDEN: mden
| MDCRD: mdcrd
|MDINFO: mdinfo
| MTMD: mtmd
|INPDIP: inpdip
|RSTDIP: rstdip
|INPTRA: inptraj
|
Here is the input file:
Initial heating and equilabration
&cntrl
imin=0, irest=0, ntx=1,ig=-1,
nstlim=100000, dt=0.001,
ntpr=100, ntwx=10,
ntr=1, restraintmask=':1-356',
restraint_wt=1.0,
cut=16.0, ntb=1, ntc=2, ntf=2,
ntt=3, gamma_ln=1.0,
tempi=0.0, temp0=300.0,
/
--------------------------------------------------------------------------------
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 = 42.146
| New format PARM file being parsed.
| Version = 1.000 Date = 09/15/12 Time = 14:48:33
NATOM = 51302 NTYPES = 16 NBONH = 48445 MBONA = 2921
NTHETH = 6483 MTHETA = 3967 NPHIH = 12725 MPHIA = 9165
NHPARM = 0 NPARM = 0 NNB = 92379 NRES = 15554
NBONA = 2921 NTHETA = 3967 NPHIA = 9165 NUMBND = 46
NUMANG = 100 NPTRA = 60 NATYP = 32 NPHB = 1
IFBOX = 1 NMXRS = 39 IFCAP = 0 NEXTRA = 0
NCOPY = 0
| Memory Use Allocated
| Real 2903690
| Hollerith 169462
| Integer 2212178
| Max Pairs 3693744
| nblistReal 615624
| nblist Int 1442864
| Total 56862 kbytes
| Note: 1-4 EEL scale factors are being read from the topology file.
| Note: 1-4 VDW scale factors are being read from the topology file.
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals
BOX TYPE: RECTILINEAR
--------------------------------------------------------------------------------
2. CONTROL DATA FOR THE RUN
--------------------------------------------------------------------------------
default_name
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 =
500
iwrap = 0, ntwx = 10, 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 = 16.00000, intdiel = 1.00000
Frozen or restrained atoms:
ibelly = 0, ntr = 1
Molecular dynamics:
nstlim = 100000, nscm = 0, nrespa = 1
t = 0.00000, dt = 0.00100, vlimit = 20.00000
Langevin dynamics temperature regulation:
ig = 708419
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 = 84.291 Box Y = 86.834 Box Z = 86.545
Alpha = 90.000 Beta = 90.000 Gamma = 90.000
NFFT1 = 90 NFFT2 = 90 NFFT3 = 90
Cutoff= 16.000 Tol =0.100E-04
Ewald Coefficient = 0.16683
Interpolation order = 4
| MPI Timing options:
| profile_mpi = 0
LOADING THE CONSTRAINED ATOMS AS GROUPS
5. REFERENCE ATOM COORDINATES
defa
Mask :1-356; matches 5708 atoms
--------------------------------------------------------------------------------
3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------
defa
begin time read from input coords = 0.000 ps
Number of triangulated 3-point waters found: 15198
| Atom division among processors:
| 0 1429 2856 4288 5708 7127 8552 9977
| 11402 12827 14252 15677 17102 18527 19952 21377
| 22802 24227 25652 27077 28502 29927 31352 32777
| 34202 35627 37052 38477 39902 41327 42752 44177
| 45602 47027 48452 49877 51302
Sum of charges from parm topology file = -0.00000036
Forcing neutrality...
| Running AMBER/MPI version on 36 nodes
| WARNING: The number of processors is not a power of 2
| this may be inefficient on some systems.
--------------------------------------------------------------------------------
4. RESULTS
--------------------------------------------------------------------------------
| # of SOLUTE degrees of freedom (RNDFP): 105461.
| # of SOLVENT degrees of freedom (RNDFS): 0.
| NDFMIN = 105461. NUM_NOSHAKE = 0 CORRECTED RNDFP = 105461.
| TOTAL # of degrees of freedom (RNDF) = 105461.
---------------------------------------------------
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 = 0.7766E-11 at 2.666360
---------------------------------------------------
| Local SIZE OF NONBOND LIST = 1615653
| TOTAL SIZE OF NONBOND LIST = 51468363
NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS =
0.0
Etot = -185731.2252 EKtot = 0.0000 EPtot =
-185731.2252
BOND = 278.8734 ANGLE = 1861.3628 DIHED =
3507.3955
1-4 NB = 2438.4476 1-4 EEL = 6914.8356 VDWAALS =
37009.0861
EELEC = -237741.2263 EHBOND = 0.0000 RESTRAINT =
0.0000
Ewald error estimate: 0.1789E-03
------------------------------------------------------------------------------
vlimit exceeded for step 67; vmax = 20.7390
vlimit exceeded for step 68; vmax = 105.2175
vlimit exceeded for step 89; vmax = 59.8578
NSTEP = 100 TIME(PS) = 0.100 TEMP(K) = 243.56 PRESS =
0.0
Etot = -141487.6349 EKtot = 25521.1288 EPtot =
-167008.7637
BOND = 8111.5156 ANGLE = 4371.5097 DIHED =
3795.6559
1-4 NB = 2021.2375 1-4 EEL = 9316.0729 VDWAALS =
30623.2087
EELEC = -227134.3588 EHBOND = 0.0000 RESTRAINT =
1886.3949
EAMBER (non-restraint) = -168895.1585
Ewald error estimate: 0.2843E-03
------------------------------------------------------------------------------
NSTEP = 200 TIME(PS) = 0.200 TEMP(K) = 331.51 PRESS =
0.0
Etot = -124044.5467 EKtot = 34737.2505 EPtot =
-158781.7972
BOND = 9703.4595 ANGLE = 4378.4662 DIHED =
3915.6569
1-4 NB = 1960.0108 1-4 EEL = 13987.4729 VDWAALS =
27722.0667
EELEC = -222427.7408 EHBOND = 0.0000 RESTRAINT =
1978.8105
EAMBER (non-restraint) = -160760.6077
Ewald error estimate: 0.2739E-03
------------------------------------------------------------------------------
vlimit exceeded for step 235; vmax = 94.6700
vlimit exceeded for step 236; vmax = 40.9201
vlimit exceeded for step 237; vmax = 21.4916
vlimit exceeded for step 240; vmax = 52.1407
vlimit exceeded for step 246; vmax = 39.3525
vlimit exceeded for step 247; vmax = 20.3228
vlimit exceeded for step 254; vmax = 23.5640
vlimit exceeded for step 255; vmax = 20.8441
vlimit exceeded for step 261; vmax = 20.6267
vlimit exceeded for step 274; vmax = 22.5507
vlimit exceeded for step 279; vmax = 22.4915
vlimit exceeded for step 280; vmax = 21.4564
vlimit exceeded for step 283; vmax = 30.4692
vlimit exceeded for step 284; vmax = 23.4604
vlimit exceeded for step 285; vmax = 127.1832
vlimit exceeded for step 286; vmax = 25.9320
vlimit exceeded for step 287; vmax = 23.7445
vlimit exceeded for step 295; vmax = 80.0427
NSTEP = 300 TIME(PS) = 0.300 TEMP(K) = 404.15 PRESS =
0.0
Etot = -111463.1861 EKtot = 42349.0483 EPtot =
-153812.2344
BOND = 8074.4844 ANGLE = 7187.0126 DIHED =
4524.8081
1-4 NB = 2285.1303 1-4 EEL = 12706.7726 VDWAALS =
28067.3422
EELEC = -220509.8177 EHBOND = 0.0000 RESTRAINT =
3852.0331
EAMBER (non-restraint) = -157664.2675
Ewald error estimate: 0.1937E-03
------------------------------------------------------------------------------
vlimit exceeded for step 300; vmax = 20.6823
vlimit exceeded for step 302; vmax = 20.4763
vlimit exceeded for step 306; vmax = 37.0253
vlimit exceeded for step 308; vmax = 27.0988
vlimit exceeded for step 309; vmax = 23.1403
vlimit exceeded for step 313; vmax = 28.6812
vlimit exceeded for step 315; vmax = 30.7255
vlimit exceeded for step 321; vmax = 20.2251
vlimit exceeded for step 326; vmax = 107.6804
vlimit exceeded for step 327; vmax = 32.2235
vlimit exceeded for step 331; vmax = 31.2923
vlimit exceeded for step 332; vmax = 20.5891
vlimit exceeded for step 334; vmax = 28.1971
vlimit exceeded for step 335; vmax = 22.9023
vlimit exceeded for step 340; vmax = 359.9275
vlimit exceeded for step 341; vmax = 28.9358
vlimit exceeded for step 342; vmax = 23.7921
vlimit exceeded for step 351; vmax = 20.5363
vlimit exceeded for step 352; vmax = 21.4512
vlimit exceeded for step 354; vmax = 66.0010
vlimit exceeded for step 355; vmax = 22.9163
vlimit exceeded for step 356; vmax = 81.6805
vlimit exceeded for step 357; vmax = 62.7346
vlimit exceeded for step 358; vmax = 118.7586
vlimit exceeded for step 359; vmax = 21.5861
vlimit exceeded for step 360; vmax = 22.8603
vlimit exceeded for step 361; vmax = 69.0441
vlimit exceeded for step 362; vmax = 29.5307
vlimit exceeded for step 363; vmax = 22.3842
vlimit exceeded for step 364; vmax = 27.7772
vlimit exceeded for step 367; vmax = 46.9652
vlimit exceeded for step 368; vmax = 27.5596
vlimit exceeded for step 371; vmax = 480.3994
vlimit exceeded for step 372; vmax = 31.6060
vlimit exceeded for step 373; vmax = 23.3520
vlimit exceeded for step 374; vmax = 20.7760
vlimit exceeded for step 375; vmax = 27.5994
vlimit exceeded for step 377; vmax = 29.6963
vlimit exceeded for step 378; vmax = 25.5789
vlimit exceeded for step 379; vmax = 230.0853
vlimit exceeded for step 380; vmax = 25.9490
vlimit exceeded for step 384; vmax = 28.6707
vlimit exceeded for step 386; vmax = 22.7463
vlimit exceeded for step 387; vmax = 21.6875
vlimit exceeded for step 388; vmax = 24.4574
On Tue, Oct 9, 2012 at 9:35 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> The fact that you are getting vlimit errors suggests that your
> previous minimization scheme was not adequate. However, without
> knowing more details about your system and what minimization you have
> already tried to do to, it's difficult to make further suggestions. I
> see that you're running with PBC off (ntb=0) and no implicit solvent
> model (igb=0) - is there a particular reason for that?
>
> -Dan
>
> On Tue, Oct 9, 2012 at 5:18 AM, Jitesh Doshi <dosjitesh.gmail.com> wrote:
> > Hi all,
> > can anyone help me out with the error discussed above? Still not through
> > with it..
> >
> > On Fri, Oct 5, 2012 at 5:41 PM, Jitesh Doshi <dosjitesh.gmail.com>
> wrote:
> >
> >> yes.. i have run minimization in two steps.. restrained and then freeing
> >> all the atoms. I am not sure as to how exactly I should start dissecting
> >> the problem. Whatever i know about amber, things seems fine except I
> don't
> >> know if something is wrong with the input file for the run which is:
> >>
> >> Initial heating and equilabration
> >> &cntrl
> >> imin=0, irest=0, ntx=1,ig=-1,
> >> nstlim=100000, dt=0.001, ntc=1,
> >> ntpr=100, ntwx=10,
> >> ntr=1, restraint_wt=1, restraintmask=':1-356',
> >> cut=16, ntb=0, igb=0,
> >> ntt=3, gamma_ln=1.0,
> >> tempi=0.0, temp0=300.0,
> >> /
> >>
> >> On Fri, Oct 5, 2012 at 5:28 PM, David A Case <case.biomaps.rutgers.edu
> >wrote:
> >>
> >>> On Fri, Oct 05, 2012, Jitesh Doshi wrote:
> >>>
> >>> > first occurrence of vlimit exceeds appears at step 159, so it runs
> >>> properly
> >>> > till 158 steps.
> >>>
> >>> This ain't necessarily so. It may just mean the problems with the
> setup
> >>> don't
> >>> become severe enough until then to trigger the warning.
> >>>
> >>> > My temperature limits are 0 to 300. and i observe that in all those
> >>> steps
> >>> > where vlimit exceeds, temperature blows off beyond 300. Could this be
> >>> the
> >>> > reason for vlimit exceeding?
> >>>
> >>> It's the other way around: bad forces or collisions are leading to
> large
> >>> local
> >>> velocities. This is turn results in high temperatures. All these are
> >>> just
> >>> symptoms....you need to examine your simulation carefully to look for
> what
> >>> might be causing the problem. Did you indeed run energy minimization
> >>> first?
> >>>
> >>> ...dac
> >>>
> >>>
> >>> _______________________________________________
> >>> AMBER mailing list
> >>> AMBER.ambermd.org
> >>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>
> >>
> >>
> >>
> >> --
> >> Jitesh V. Doshi
> >> Research Associate,
> >> Bioinformatics Centre,
> >> University of Pune.
> >>
> >>
> >
> >
> > --
> > Jitesh V. Doshi
> > Research Associate,
> > Bioinformatics Centre,
> > University of Pune.
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 201
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-9119 (Fax)
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jitesh V. Doshi
Research Associate,
Bioinformatics Centre,
University of Pune.
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Received on Wed Oct 10 2012 - 03:30:02 PDT
