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From: Hannes Loeffler <Hannes.Loeffler.stfc.ac.uk>

Date: Mon, 29 Aug 2016 20:26:33 +0100

Hi,

many thanks for your interest in tutorial A9.

I cannot reproduce this error but admittedly the "equilibration" time

was deliberately set as short as possible for the sake of a tutorial.

So, what you can try is to increase the number of steps in the prior

steps i.e. minimization and heatind and if necessary reduce the

integration time step (dt) to, say, 0.001 to see if you can get a more

stable simulation.

Cheers,

Hannes.

On Mon, 29 Aug 2016 22:26:56 +0800

张姝姝 <roseshu8430.163.com> wrote:

*> 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
*

*>
*

*>
*

*>
*

*>
*

*>
*

*> _______________________________________________
*

*> AMBER mailing list
*

*> AMBER.ambermd.org
*

*> http://lists.ambermd.org/mailman/listinfo/amber
*

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Received on Mon Aug 29 2016 - 12:30:05 PDT

Date: Mon, 29 Aug 2016 20:26:33 +0100

Hi,

many thanks for your interest in tutorial A9.

I cannot reproduce this error but admittedly the "equilibration" time

was deliberately set as short as possible for the sake of a tutorial.

So, what you can try is to increase the number of steps in the prior

steps i.e. minimization and heatind and if necessary reduce the

integration time step (dt) to, say, 0.001 to see if you can get a more

stable simulation.

Cheers,

Hannes.

On Mon, 29 Aug 2016 22:26:56 +0800

张姝姝 <roseshu8430.163.com> wrote:

_______________________________________________

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AMBER.ambermd.org

http://lists.ambermd.org/mailman/listinfo/amber

Received on Mon Aug 29 2016 - 12:30:05 PDT

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