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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