Dear all,<br> 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. <br>
<br>Input file :<br><br>&FORCE_EVAL<br> METHOD Quickstep<br> &DFT<br> BASIS_SET_FILE_NAME BASIS_MOLOPT<br> POTENTIAL_FILE_NAME POTENTIAL<br> CHARGE = 0 <br> &MGRID<br> CUTOFF 280<br> NGRIDS 5 <br>
REL_CUTOFF 40<br> &END MGRID<br> &QS<br> METHOD GPW<br> EPS_DEFAULT 1.0E-10<br> &END QS<br> &SCF<br> SCF_GUESS RESTART<br> EPS_SCF 1.0E-6<br> MAX_SCF 150<br>
# MIXING 0.3<br> &OUTER_SCF<br> EPS_SCF 1.0E-6<br> MAX_SCF 50<br> &END<br> &OT<br> MINIMIZER CG<br> PRECONDITIONER FULL_ALL<br> ENERGY_GAP 0.001<br>
STEPSIZE 0.05<br> &END<br> <br> &END SCF<br> &XC<br> &XC_FUNCTIONAL BLYP <br> &END XC_FUNCTIONAL<br> &XC_GRID<br> XC_SMOOTH_RHO NN50<br> XC_DERIV SPLINE2<br>
&END<br> &vdW_POTENTIAL<br> DISPERSION_FUNCTIONAL PAIR_POTENTIAL<br> &PAIR_POTENTIAL<br> TYPE DFTD2<br> REFERENCE_FUNCTIONAL BLYP <br> &END PAIR_POTENTIAL<br>
&END vdW_POTENTIAL<br> <br> &END XC<br> &END DFT<br><br> &SUBSYS<br> &CELL <br> ABC 12.16174 12.16174 12.16174<br> &END CELL<br><br> &COORD<br> @INCLUDE coor.xyz <br>
&END COORD<br><br> &KIND O<br> BASIS_SET TZV2P-MOLOPT-GTH-q6 <br> POTENTIAL GTH-BLYP-q6<br> &END KIND<br> <br> &KIND C<br> BASIS_SET TZV2P-MOLOPT-GTH-q4 <br> POTENTIAL GTH-BLYP-q4<br>
&END KIND<br><br> &KIND H<br> BASIS_SET TZV2P-MOLOPT-GTH-q1 <br> POTENTIAL GTH-BLYP-q1<br># MASS 2.016<br> &END KIND<br><br> &COLVAR<br> &TORSION <br> ATOMS 179 178 181 180 <br>
&END <br> &END<br> &COLVAR<br> &DISTANCE<br> ATOMS 180 181 <br> &END<br> &END <br> &COLVAR<br> &TORSION<br> ATOMS 179 178 182 183 <br> &END <br>
&END<br> &COLVAR<br> &DISTANCE<br> ATOMS 182 183 <br> &END<br> &END <br> <br><br> &END SUBSYS<br>&END FORCE_EVAL<br><br>&GLOBAL<br> PROJECT OUT-CA-AA-MD<br> RUN_TYPE MD<br>
PRINT_LEVEL MEDIUM<br>&END GLOBAL<br><br>&MOTION<br> &MD<br> ENSEMBLE NVT<br> STEPS 10000<br> TIMESTEP 0.5<br> &THERMOSTAT<br> &NOSE<br> LENGTH 3<br> YOSHIDA 3<br> TIMECON 100.0<br>
MTS 2<br> &END NOSE<br> &END THERMOSTAT<br> TEMPERATURE 300.0 <br> &END MD<br> <br> &FREE_ENERGY<br> &METADYN<br> DO_HILLS .FALSE.<br> &METAVAR<br> COLVAR 1 <br>
SCALE 1.<br> &END <br> &PRINT<br> &COLVAR<br> COMMON_ITERATION_LEVELS 3<br> &EACH<br> MD 1<br> &END<br> &END<br> &END <br>
&METAVAR<br> COLVAR 2 <br> SCALE 1.<br> &END <br> &PRINT<br> &COLVAR<br> COMMON_ITERATION_LEVELS 3<br> &EACH<br> MD 1<br> &END<br>
&END<br> &END<br> &METAVAR<br> COLVAR 2 <br> SCALE 1.<br> &END <br> &PRINT<br> &COLVAR<br> COMMON_ITERATION_LEVELS 3<br> &EACH<br>
MD 1<br> &END<br> &END<br> &END<br> &METAVAR<br> COLVAR 3 <br> SCALE 1.<br> &END <br> &PRINT<br> &COLVAR<br> COMMON_ITERATION_LEVELS 3<br>
&EACH<br> MD 1<br> &END<br> &END<br> &END<br> &END<br> &END<br><br> &CONSTRAINT<br> &CONSTRAINT_INFO<br> &EACH<br> MD 1<br>
&END<br> &END <br> &COLLECTIVE<br> COLVAR 1 <br> INTERMOLECULAR 1 <br> TARGET 0.00 <br> TARGET_GROWTH 0.001 <br> TARGET_LIMIT 0.872647<br> &RESTRAINT<br> K [kcalmol] 20.0000 <br>
&END<br> &END<br> &END<br> &PRINT<br> &VELOCITIES<br> &EACH<br> MD 1<br> &END<br> &END<br> &FORCES<br> &EACH<br> MD 1 <br> &END <br>
&END<br> &END<br><br>&END MOTION<br><br>&EXT_RESTART<br> RESTART_FILE_NAME OUT-CA-AA-MD-1.restart<br> RESTART_COUNTERS T<br> RESTART_POS T<br> RESTART_VEL T <br> RESTART_CONSTRAINT T<br>
RESTART_METADYNAMICS F <br>&END EXT_RESTART<br><br><br>-------------- <br><br>Before restart, the COLVAR file contains .. <br><br><br> 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<br>
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<br> 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<br>
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<br> 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<br>
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<br> 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<br>
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<br> 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<br>
<br><br>After restart, <br><br> <br> 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<br>
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<br> 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<br>
<br><br>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 <br><br>Before restart, <br><br> 2941 1470.500000 0.264232649 305.633596492 -1071.124343277 -1070.837205951 110.006900000<br>
2942 1471.000000 0.262352431 303.458778818 -1071.122443287 -1070.837141220 126.382300000<br> 2943 1471.500000 0.258554740 299.066050830 -1071.118558109 -1070.837008858 109.594400000<br>
2944 1472.000000 0.254843481 294.773298732 -1071.114769705 -1070.836887261 108.996200000<br> 2945 1472.500000 0.253037023 292.683797430 -1071.112972727 -1070.836852718 109.157400000<br>
2946 1473.000000 0.253686059 293.434527505 -1071.113732934 -1070.836919998 125.062900000<br> 2947 1473.500000 0.255812040 295.893615199 -1071.116023855 -1070.837040816 108.843300000<br>
2948 1474.000000 0.257604549 297.966981110 -1071.117955614 -1070.837135519 125.324700000<br><br><br>after restart, <br><br><br> 2941 1470.500000 0.264119595 305.502828525 -1071.124357212 -1070.837332951 540.249300000<br>
2942 1471.000000 0.262260456 303.352392372 -1071.122478947 -1070.837268889 203.759400000<br> 2943 1471.500000 0.258489935 298.991092511 -1071.118620866 -1070.837136476 203.167400000<br>
2944 1472.000000 0.254807453 294.731625484 -1071.114861358 -1070.837015022 178.069300000<br><br><br><br>Can anybody help me out how to restart the job?<br><br>Thanks.<br><br>Regards,<br>
Sandeep<br>