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
