Restart MD
Sandeep Kumar Reddy
kuma... at gmail.com
Wed Nov 23 06:28:54 UTC 2011
Dear all,
I am doing an MD run by restraining dihedral to some value. I
have a problem with restarting this job. When i used the following options
to restart this, the value of COLVAR 1 before and after restart are not
same.
Input file :
&FORCE_EVAL
METHOD Quickstep
&DFT
BASIS_SET_FILE_NAME BASIS_MOLOPT
POTENTIAL_FILE_NAME POTENTIAL
CHARGE = 0
&MGRID
CUTOFF 280
NGRIDS 5
REL_CUTOFF 40
&END MGRID
&QS
METHOD GPW
EPS_DEFAULT 1.0E-10
&END QS
&SCF
SCF_GUESS RESTART
EPS_SCF 1.0E-6
MAX_SCF 150
# MIXING 0.3
&OUTER_SCF
EPS_SCF 1.0E-6
MAX_SCF 50
&END
&OT
MINIMIZER CG
PRECONDITIONER FULL_ALL
ENERGY_GAP 0.001
STEPSIZE 0.05
&END
&END SCF
&XC
&XC_FUNCTIONAL BLYP
&END XC_FUNCTIONAL
&XC_GRID
XC_SMOOTH_RHO NN50
XC_DERIV SPLINE2
&END
&vdW_POTENTIAL
DISPERSION_FUNCTIONAL PAIR_POTENTIAL
&PAIR_POTENTIAL
TYPE DFTD2
REFERENCE_FUNCTIONAL BLYP
&END PAIR_POTENTIAL
&END vdW_POTENTIAL
&END XC
&END DFT
&SUBSYS
&CELL
ABC 12.16174 12.16174 12.16174
&END CELL
&COORD
@INCLUDE coor.xyz
&END COORD
&KIND O
BASIS_SET TZV2P-MOLOPT-GTH-q6
POTENTIAL GTH-BLYP-q6
&END KIND
&KIND C
BASIS_SET TZV2P-MOLOPT-GTH-q4
POTENTIAL GTH-BLYP-q4
&END KIND
&KIND H
BASIS_SET TZV2P-MOLOPT-GTH-q1
POTENTIAL GTH-BLYP-q1
# MASS 2.016
&END KIND
&COLVAR
&TORSION
ATOMS 179 178 181 180
&END
&END
&COLVAR
&DISTANCE
ATOMS 180 181
&END
&END
&COLVAR
&TORSION
ATOMS 179 178 182 183
&END
&END
&COLVAR
&DISTANCE
ATOMS 182 183
&END
&END
&END SUBSYS
&END FORCE_EVAL
&GLOBAL
PROJECT OUT-CA-AA-MD
RUN_TYPE MD
PRINT_LEVEL MEDIUM
&END GLOBAL
&MOTION
&MD
ENSEMBLE NVT
STEPS 10000
TIMESTEP 0.5
&THERMOSTAT
&NOSE
LENGTH 3
YOSHIDA 3
TIMECON 100.0
MTS 2
&END NOSE
&END THERMOSTAT
TEMPERATURE 300.0
&END MD
&FREE_ENERGY
&METADYN
DO_HILLS .FALSE.
&METAVAR
COLVAR 1
SCALE 1.
&END
&PRINT
&COLVAR
COMMON_ITERATION_LEVELS 3
&EACH
MD 1
&END
&END
&END
&METAVAR
COLVAR 2
SCALE 1.
&END
&PRINT
&COLVAR
COMMON_ITERATION_LEVELS 3
&EACH
MD 1
&END
&END
&END
&METAVAR
COLVAR 2
SCALE 1.
&END
&PRINT
&COLVAR
COMMON_ITERATION_LEVELS 3
&EACH
MD 1
&END
&END
&END
&METAVAR
COLVAR 3
SCALE 1.
&END
&PRINT
&COLVAR
COMMON_ITERATION_LEVELS 3
&EACH
MD 1
&END
&END
&END
&END
&END
&CONSTRAINT
&CONSTRAINT_INFO
&EACH
MD 1
&END
&END
&COLLECTIVE
COLVAR 1
INTERMOLECULAR 1
TARGET 0.00
TARGET_GROWTH 0.001
TARGET_LIMIT 0.872647
&RESTRAINT
K [kcalmol] 20.0000
&END
&END
&END
&PRINT
&VELOCITIES
&EACH
MD 1
&END
&END
&FORCES
&EACH
MD 1
&END
&END
&END
&END MOTION
&EXT_RESTART
RESTART_FILE_NAME OUT-CA-AA-MD-1.restart
RESTART_COUNTERS T
RESTART_POS T
RESTART_VEL T
RESTART_CONSTRAINT T
RESTART_METADYNAMICS F
&END EXT_RESTART
--------------
Before restart, the COLVAR file contains ..
1470.0 0.70287 2.00213 2.00213 -0.23927
0.00000 0.00000 0.00000 0.00000 0.00000
0.00000 0.00000 0.00000 0.00000 0.00000
1470.5 0.70864 1.98593 1.98593 -0.23249
0.00000 0.00000 0.00000 0.00000 0.00000
0.00000 0.00000 0.00000 0.00000 0.00000
1471.0 0.71401 1.96755 1.96755 -0.22558
0.00000 0.00000 0.00000 0.00000 0.00000
0.00000 0.00000 0.00000 0.00000 0.00000
1471.5 0.71885 1.94803 1.94803 -0.21857
0.00000 0.00000 0.00000 0.00000 0.00000
0.00000 0.00000 0.00000 0.00000 0.00000
1472.0 0.72302 1.92860 1.92860 -0.21149
0.00000 0.00000 0.00000 0.00000 0.00000
0.00000 0.00000 0.00000 0.00000 0.00000
1472.5 0.72638 1.91055 1.91055 -0.20437
0.00000 0.00000 0.00000 0.00000 0.00000
0.00000 0.00000 0.00000 0.00000 0.00000
1473.0 0.72881 1.89520 1.89520 -0.19724
0.00000 0.00000 0.00000 0.00000 0.00000
0.00000 0.00000 0.00000 0.00000 0.00000
1473.5 0.73017 1.88373 1.88373 -0.19014
0.00000 0.00000 0.00000 0.00000 0.00000
0.00000 0.00000 0.00000 0.00000 0.00000
1474.0 0.73037 1.87703 1.87703 -0.18308
0.00000 0.00000 0.00000 0.00000 0.00000
0.00000 0.00000 0.00000 0.00000 0.00000
After restart,
1470.5 0.70596 1.98584 1.98584 -0.23193
0.00000 0.00000 0.00000 0.00000 0.00000
0.00000 0.00000 0.00000 0.00000 0.00000
1471.0 0.70867 1.96732 1.96732 -0.22446
0.00000 0.00000 0.00000 0.00000 0.00000
0.00000 0.00000 0.00000 0.00000 0.00000
1471.5 0.71088 1.94763 1.94763 -0.21691
0.00000 0.00000 0.00000 0.00000 0.00000
0.00000 0.00000 0.00000 0.00000 0.00000
As can be seen, COLVAR1 value is not same at 1470.5, 1471.0 so on .. th
time step. And also, ener file output is
Before restart,
2941 1470.500000 0.264232649 305.633596492
-1071.124343277 -1070.837205951 110.006900000
2942 1471.000000 0.262352431 303.458778818
-1071.122443287 -1070.837141220 126.382300000
2943 1471.500000 0.258554740 299.066050830
-1071.118558109 -1070.837008858 109.594400000
2944 1472.000000 0.254843481 294.773298732
-1071.114769705 -1070.836887261 108.996200000
2945 1472.500000 0.253037023 292.683797430
-1071.112972727 -1070.836852718 109.157400000
2946 1473.000000 0.253686059 293.434527505
-1071.113732934 -1070.836919998 125.062900000
2947 1473.500000 0.255812040 295.893615199
-1071.116023855 -1070.837040816 108.843300000
2948 1474.000000 0.257604549 297.966981110
-1071.117955614 -1070.837135519 125.324700000
after restart,
2941 1470.500000 0.264119595 305.502828525
-1071.124357212 -1070.837332951 540.249300000
2942 1471.000000 0.262260456 303.352392372
-1071.122478947 -1070.837268889 203.759400000
2943 1471.500000 0.258489935 298.991092511
-1071.118620866 -1070.837136476 203.167400000
2944 1472.000000 0.254807453 294.731625484
-1071.114861358 -1070.837015022 178.069300000
Can anybody help me out how to restart the job?
Thanks.
Regards,
Sandeep
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