[gmx-users] cpmd dynamics
Justin Lemkul
jalemkul at vt.edu
Wed Jan 23 19:46:41 CET 2013
On 1/23/13 1:43 PM, Debashis Sahu wrote:
> Dear user,
> Now I am trying a dynamics of a simple molecule binding with
> an halide in gas phase in normal cpmd without any interface of
> gromacs-cpmd. But this MD is not running properly after 15 steps. The
If you are working directly with CPMD, you should be posting to their mailing list.
-Justin
> output of this MD is following type :
> * simple molecular dynamics deltat=4au
> *
> ******************************************************************************
>
> CAR-PARRINELLO MOLECULAR DYNAMICS
>
> PATH TO THE RESTART FILES: ./
> RESTART WITH OLD ORBITALS
> RESTART WITH OLD ION POSITIONS
> RESTART WITH LATEST RESTART FILE
> ITERATIVE ORTHOGONALIZATION
> MAXIT: 30
> EPS: 1.00E-06
> MAXIMUM NUMBER OF STEPS: 10000 STEPS
> PRINT INTERMEDIATE RESULTS EVERY 10001 STEPS
> STORE INTERMEDIATE RESULTS EVERY 10001 STEPS
> STORE INTERMEDIATE RESULTS EVERY 10001 SELF-CONSISTENT STEPS
> NUMBER OF DISTINCT RESTART FILES: 1
> TEMPERATURE IS CALCULATED ASSUMING AN ISOLATED MOLECULE
> FICTITIOUS ELECTRON MASS: 400.0000
> TIME STEP FOR ELECTRONS: 5.0000
> TIME STEP FOR IONS: 5.0000
> TRAJECTORIES ARE SAVED ON FILE
> TRAJEC.xyz IS SAVED ON FILE
> ELECTRON DYNAMICS: THE TEMPERATURE IS NOT CONTROLLED
> ION DYNAMICS: THE TEMPERATURE IS NOT CONTROLLED
> SPLINE INTERPOLATION IN G-SPACE FOR PSEUDOPOTENTIAL FUNCTIONS
> NUMBER OF SPLINE POINTS: 5000
>
> EXCHANGE CORRELATION FUNCTIONALS
> LDA EXCHANGE: SLATER (ALPHA = 0.66667)
> LDA CORRELATION: LEE, YANG & PARR
> [C.L. LEE, W. YANG, AND R.G. PARR, PRB 37 785 (1988)]
> GRADIENT CORRECTED FUNCTIONAL
> DENSITY THRESHOLD: 1.00000E-08
> EXCHANGE ENERGY
> [A.D. BECKE, PHYS. REV. A 38, 3098 (1988)]
> PARAMETER BETA: 0.004200
> CORRELATION ENERGY
> [LYP: C.L. LEE ET AL. PHYS. REV. B 37, 785 (1988)]
>
> *** DETSP| SIZE OF THE PROGRAM IS 8564/ 219400 kBYTES ***
>
> >>>>>>>> CENTER OF MASS HAS BEEN MOVED TO CENTER OF BOX <<<<<<<<
> TOTAL INTEGRATED ELECTRONIC DENSITY
> IN G-SPACE = 32.000000
> IN R-SPACE = 32.000000
>
> (K+E1+L+N+X) TOTAL ENERGY = -67.09114118 A.U.
> (K) KINETIC ENERGY = 51.98353287 A.U.
> (E1=A-S+R) ELECTROSTATIC ENERGY = -47.02753506 A.U.
> (S) ESELF = 51.53004455 A.U.
> (R) ESR = 2.07472788 A.U.
> (L) LOCAL PSEUDOPOTENTIAL ENERGY = -60.56675780 A.U.
> (N) N-L PSEUDOPOTENTIAL ENERGY = 5.23968996 A.U.
> (X) EXCHANGE-CORRELATION ENERGY = -16.72007115 A.U.
> GRADIENT CORRECTION ENERGY = -0.91529031 A.U.
>
> NFI EKINC TEMPP EKS ECLASSIC EHAM
> DIS TCPU
> 1 0.03372 1.3 -67.09114 -67.09110 -67.05738
> 0.219E-07 4.12
> FILE TRAJECTORY EXISTS, NEW DATA WILL BE APPENDED
> FILE TRAJEC.xyz EXISTS, NEW DATA WILL BE APPENDED
> 2 0.08543 4.3 -67.14733 -67.14719 -67.06176
> 0.331E-06 4.13
> 3 0.09756 7.5 -67.15818 -67.15793 -67.06037
> 0.153E-05 4.09
> 4 0.08281 9.7 -67.14102 -67.14070 -67.05789
> 0.431E-05 4.09
> 5 0.07448 10.6 -67.13244 -67.13209 -67.05761
> 0.912E-05 4.13
> 6 0.07775 10.3 -67.13636 -67.13602 -67.05827
> 0.160E-04 4.10
> 7 0.07992 9.3 -67.13746 -67.13715 -67.05723
> 0.247E-04 4.12
> 8 0.07661 8.0 -67.12951 -67.12925 -67.05263
> 0.344E-04 4.12
> 9 0.07345 6.8 -67.11278 -67.11255 -67.03910
> 0.444E-04 4.12
> 10 0.07518 6.3 -67.07105 -67.07084 -66.99566
> 0.540E-04 4.12
> 11 0.08715 6.5 -66.93991 -66.93970 -66.85254
> 0.633E-04 4.13
> 12 0.12795 7.5 -66.50634 -66.50609 -66.37814
> 0.724E-04 4.11
> 13 0.26154 9.1 -65.05321 -65.05291 -64.79136
> 0.826E-04 4.14
> 14 0.69724 10.9 -60.05817 -60.05781 -59.36057
> 0.945E-04 4.15
> 15 1.85716 12.3 -40.98691 -40.98650 -39.12934
> 0.109E-03 4.15
> 16 NaN NaN NaN NaN NaN
> 0.124E-03 3.78
> 17 NaN NaN NaN NaN NaN NaN
> 3.78
> 18 NaN NaN NaN NaN NaN NaN
> 3.78
> 19 NaN NaN NaN NaN NaN NaN
> 3.80
> 20 NaN NaN NaN NaN NaN NaN
> 3.77
> 21 NaN NaN NaN NaN NaN NaN
> 3.77
> 22 NaN NaN NaN NaN NaN NaN
> 3.78
> 23 NaN NaN NaN NaN NaN NaN
> 3.78
>
> I have used the following MD input in cpmd -----
>
>
> &CPMD
> MOLECULAR DYNAMICS CP
> ISOLATED MOLECULE
> RESTART WAVEFUNCTION COORDINATES LATEST
> TRAJECTORY XYZ
> &END
>
> QUENCH BO
> ANNEALING IONS
> 0.99
> TEMPERATURE
> 300
> EMASS
> 600.
> TIMESTEP
> 5.0
> MAXSTEP
> 10000
> TRAJECTORY SAMPLE
> 0
> STORE
> 100
> RESTFILE
> 1
> &END
>
> &DFT
> FUNCTIONAL BLYP
> &END
>
> &SYSTEM
> ANGSTROM
> POISSON SOLVER TUCKERMAN
> SYMMETRY
> 0
> SYMMETRY
> 0
> CELL
> 11.0 1.0 1.0 0 0 0
> CUTOFF
> 70.0
> CHARGE
> -1.0
> ENERGY PROFILE
> &END
>
> Plz, help me to solve this problem.
>
>
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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