(unknown charset) [AMBER] errors in doing TI tutorial calculation

From: (unknown charset) 张姝姝 <roseshu8430.163.com>
Date: Mon, 29 Aug 2016 22:26:56 +0800 (CST)

Dear list,


I am trying to do the tutorial of TI calculation. I have downloaded all the setup files and followed the steps in the "sander" fold.
I went through the minimization, heat, press steps for ligands,
but errors came out when pressing for the complex, while the heating steps for complex seem to finish normally.
"vlimit exceeded for step 673; vmax = 48.8156


     Coordinate resetting (SHAKE) cannot be accomplished,
     deviation is too large
     NITER, NIT, LL, I and J are : 0 3 239 474 473


     Note: This is usually a symptom of some deeper
     problem with the energetics of the system."


How to deal with it? Any help would be highly appreciated.



Thank you for your help.
Shushu Zhang


I pasted the whole output below.
          -------------------------------------------------------
          Amber 12 SANDER 2012
          -------------------------------------------------------


| Run on 08/29/2016 at 21:21:38
  [-O]verwriting output


File Assignments:
| MDIN: press0.in
| MDOUT: press0.out
|INPCRD: heat0.rst7
| PARM: ../complex0.parm7
|RESTRT: press0.rst7
| REFC: ../complex0.rst7
| MDVEL: mdvel.000
| MDEN: press0.en
| MDCRD: press0.nc
|MDINFO: press0.info
| MTMD: mtmd
|INPDIP: inpdip
|RSTDIP: rstdip


|INPTRA: inptraj
|


 Here is the input file:


pressurising
 &cntrl
   imin = 0, nstlim = 10000, irest = 1, ntx = 5, dt = 0.002,
   ntt = 1, temp0 = 300.0, tautp = 1.0,
   ntp = 1, pres0 = 1.0, taup = 2.0,
   ntb = 2,
   ntc = 2, ntf = 1,
   ioutfm = 1, iwrap = 1,
   ntwe = 1000, ntwx = 1000, ntpr = 1000, ntwr = 5000,


   ntr = 1, restraint_wt = 5.00
   restraintmask='!:WAT & !.H=',


   icfe = 1, ifsc = 1, clambda = 0.5, scalpha = 0.5, scbeta = 12.0,
   logdvdl = 0,
   scmask = ':1.H6'
 /
 &ewald
 /



--------------------------------------------------------------------------------
   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 = 33.230
| New format PARM file being parsed.
| Version = 1.000 Date = 08/05/16 Time = 17:09:01
 NATOM = 30532 NTYPES = 17 NBONH = 29228 MBONA = 1316
 NTHETH = 2981 MTHETA = 1771 NPHIH = 5826 MPHIA = 4392
 NHPARM = 0 NPARM = 0 NNB = 51576 NRES = 9474
 NBONA = 1316 NTHETA = 1771 NPHIA = 4392 NUMBND = 43
 NUMANG = 88 NPTRA = 41 NATYP = 31 NPHB = 1
 IFBOX = 1 NMXRS = 24 IFCAP = 0 NEXTRA = 0
 NCOPY = 0


| Memory Use Allocated
| Real 1825732
| Hollerith 101072
| Integer 1214152
| Max Pairs 1272166
| nblistReal 366384
| nblist Int 1294213
| Total 32288 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 = 5, irest = 1, ntrx = 1


Nature and format of output:
     ntxo = 1, ntpr = 1000, ntrx = 1, ntwr = 5000
     iwrap = 1, ntwx = 1000, ntwv = 0, ntwe = 1000
     ioutfm = 1, ntwprt = 0, idecomp = 0, rbornstat= 0


Potential function:
     ntf = 1, ntb = 2, igb = 0, nsnb = 25
     ipol = 0, gbsa = 0, iesp = 0
     dielc = 1.00000, cut = 8.00000, intdiel = 1.00000


Frozen or restrained atoms:
     ibelly = 0, ntr = 1
     restraint_wt = 5.00000


Molecular dynamics:
     nstlim = 10000, nscm = 0, nrespa = 1
     t = 0.00000, dt = 0.00200, vlimit = 20.00000


Berendsen (weak-coupling) temperature regulation:
     temp0 = 300.00000, tempi = 0.00000, tautp = 1.00000


Pressure regulation:
     ntp = 1
     pres0 = 1.00000, comp = 44.60000, taup = 2.00000


SHAKE:
     ntc = 2, jfastw = 0
     tol = 0.00001


Free energy options:
     icfe = 1, ifsc = 1, klambda = 1
     clambda = 0.5000, scalpha = 0.5000, scbeta = 12.0000
     sceeorder = 2 dvdl_norest = 0
     dynlmb = 0.0000 logdvdl = 0


Ewald parameters:
     verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1
     vdwmeth = 1, eedmeth = 1, netfrc = 1
     Box X = 66.461 Box Y = 70.863 Box Z = 79.558
     Alpha = 90.000 Beta = 90.000 Gamma = 90.000
     NFFT1 = 72 NFFT2 = 72 NFFT3 = 80
     Cutoff= 8.000 Tol =0.100E-04
     Ewald Coefficient = 0.34864
     Interpolation order = 4


| MPI Timing options:
| profile_mpi = 0


    LOADING THE CONSTRAINED ATOMS AS GROUPS



   5. REFERENCE ATOM COORDINATES


  defa
     Mask !:WAT & !.H=; matches 1304 atoms


--------------------------------------------------------------------------------
   3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------


default_name
 begin time read from input coords = 20.000 ps


 Number of triangulated 3-point waters found: 9303
| Atom division among processors:
| 0 3817 7633 11449 15265 19081 22900 26716
| 30532


     Softcore Mask :1.H6; matches 1 atoms
     this run corresponds to V0, its softcore atoms interact fully for lambda=0
     this process: 30532 atoms, partner process: 30533 atoms
     Checking for mismatched coordinates.
     WARNING: Local coordinate 8034 differs from partner coordinate 8037 !
     Deviation is small, changing partner coordinate.
     WARNING: Local coordinate 8037 differs from partner coordinate 8040 !
     Deviation is small, changing partner coordinate.
     WARNING: Local coordinate 8040 differs from partner coordinate 8043 !
     Deviation is small, changing partner coordinate.
     WARNING: Local coordinate 11418 differs from partner coordinate 11421 !
     Deviation is small, changing partner coordinate.
     WARNING: Local coordinate 11421 differs from partner coordinate 11424 !
     Deviation is small, changing partner coordinate.
     WARNING: Local coordinate 11424 differs from partner coordinate 11427 !
     Deviation is small, changing partner coordinate.
     WARNING: Local coordinate 11454 differs from partner coordinate 11457 !
     Deviation is small, changing partner coordinate.
     WARNING: Local coordinate 11457 differs from partner coordinate 11460 !
     Deviation is small, changing partner coordinate.
     WARNING: Local coordinate 11460 differs from partner coordinate 11463 !
     Deviation is small, changing partner coordinate.
     ... making more adjustments ...
     A total of 987 small coordinate adjustments were made, check results carefully.
     Molecule 1 is partially softcore on this side or the corresponding partner molecule is.
     Checking for SHAKE constraints on bonds crossing into the SC region
   Removing shake constraints from H6 BNZ 1 -- C6 BNZ 1


     Sum of charges for TI region 1 = -0.00000007
     Forcing neutrality...



     Sum of charges for TI region 2 = 0.00000093
     Forcing neutrality...


| Running AMBER/MPI version on 8 nodes


| MULTISANDER: 2 groups. 8 processors out of 16 total.


--------------------------------------------------------------------------------
   4. RESULTS
--------------------------------------------------------------------------------


| # of SOLUTE degrees of freedom (RNDFP): 62368.
| # of SOLVENT degrees of freedom (RNDFS): 0.
| NDFMIN = 62369. NUM_NOSHAKE = 1 CORRECTED RNDFP = 62369.
| TOTAL # of degrees of freedom (RNDF) = 62369.
   DOF for the SC part of the system: 3
 ---------------------------------------------------
 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 = 0.8332E-11 at 2.782960
 ---------------------------------------------------
| Local SIZE OF NONBOND LIST = 764013
| TOTAL SIZE OF NONBOND LIST = 5797316
vlimit exceeded for step 673; vmax = 48.8156


     Coordinate resetting (SHAKE) cannot be accomplished,
     deviation is too large
     NITER, NIT, LL, I and J are : 0 3 239 474 473


     Note: This is usually a symptom of some deeper
     problem with the energetics of the system.







--
Shushu Zhang
Sun Yat-Sen University
132 East Circle at University City
Guangzhou, China 510006
 
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Received on Mon Aug 29 2016 - 07:30:02 PDT
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