Hi,<br> Since this system is big and takes to time to execute, i prepared two water molecules system which will run very fast.<br><br>Please find the enclosed files. One (run-20steps.tar.gz) is run for 20 steps. And the other (run-10steps.tar.gz) is run for 10 steps intially, and later, it is ran for 10 steps by making restart option active. <br>
<br>Comparing COLVAR files in both of them (run-20steps & run-10steps/restart) show the differences from 11th step onwards.<br><br>Following is the differences between two files.<br><br><b>run-20steps </b><br><br> 0.0 5.66918 0.00000 0.00000 0.00000 0.00000<br>
0.5 5.66873 0.00000 0.00000 0.00000 0.00000<br> 1.0 5.67069 0.00000 0.00000 0.00000 0.00000<br> 1.5 5.67606 0.00000 0.00000 0.00000 0.00000<br>
2.0 5.68504 0.00000 0.00000 0.00000 0.00000<br> 2.5 5.69723 0.00000 0.00000 0.00000 0.00000<br> 3.0 5.71350 0.00000 0.00000 0.00000 0.00000<br>
3.5 5.73302 0.00000 0.00000 0.00000 0.00000<br> 4.0 5.75500 0.00000 0.00000 0.00000 0.00000<br> 4.5 5.78081 0.00000 0.00000 0.00000 0.00000<br>
5.0 5.80860 0.00000 0.00000 0.00000 0.00000<br> 5.5 5.83979 0.00000 0.00000 0.00000 0.00000<br> 6.0 5.87412 0.00000 0.00000 0.00000 0.00000<br>
6.5 5.91052 0.00000 0.00000 0.00000 0.00000<br> 7.0 5.95146 0.00000 0.00000 0.00000 0.00000<br> 7.5 5.99398 0.00000 0.00000 0.00000 0.00000<br>
8.0 6.03912 0.00000 0.00000 0.00000 0.00000<br> 8.5 6.08574 0.00000 0.00000 0.00000 0.00000<br> 9.0 6.13265 0.00000 0.00000 0.00000 0.00000<br>
9.5 6.18166 0.00000 0.00000 0.00000 0.00000<br> 10.0 6.23256 0.00000 0.00000 0.00000 0.00000<br><br><b>run-10steps/restart :</b><br><br><br> 0.0 5.66918 0.00000 0.00000 0.00000 0.00000<br>
0.5 5.66873 0.00000 0.00000 0.00000 0.00000<br> 1.0 5.67069 0.00000 0.00000 0.00000 0.00000<br> 1.5 5.67606 0.00000 0.00000 0.00000 0.00000<br>
2.0 5.68504 0.00000 0.00000 0.00000 0.00000<br> 2.5 5.69723 0.00000 0.00000 0.00000 0.00000<br> 3.0 5.71350 0.00000 0.00000 0.00000 0.00000<br>
3.5 5.73302 0.00000 0.00000 0.00000 0.00000<br> 4.0 5.75500 0.00000 0.00000 0.00000 0.00000<br> 4.5 5.78081 0.00000 0.00000 0.00000 0.00000<br>
5.0 5.80860 0.00000 0.00000 0.00000 0.00000<br> 5.0 5.80860 0.00000 0.00000 0.00000 0.00000<br> 5.5 5.83553 0.00000 0.00000 0.00000 0.00000<br>
6.0 5.86568 0.00000 0.00000 0.00000 0.00000<br> 6.5 5.89804 0.00000 0.00000 0.00000 0.00000<br> 7.0 5.93505 0.00000 0.00000 0.00000 0.00000<br>
7.5 5.97381 0.00000 0.00000 0.00000 0.00000<br> 8.0 6.01535 0.00000 0.00000 0.00000 0.00000<br> 8.5 6.05853 0.00000 0.00000 0.00000 0.00000<br>
9.0 6.10216 0.00000 0.00000 0.00000 0.00000<br> 9.5 6.14804 0.00000 0.00000 0.00000 0.00000<br> 10.0 6.19596 0.00000 0.00000 0.00000 0.00000<br>
<br><br>Regards,<br>Sandeep<br><br>On Nov 23, 11:45 am, Teodoro Laino <<a href="mailto:teodor...@gmail.com">teodor...@gmail.com</a>> wrote:<br>> provide an input file (+ all necessary files) that runs quickly (let's say not more than 1 minute serial), that shows the problem, with detailed info on how to do to reproduce the error you see.<br>
> Teo<br>> <br>> On Nov 23, 2011, at 7:28 AM, Sandeep Kumar Reddy wrote:<br>> <br>> <br>> <br>> <br>> <br>> <br>> <br>> > 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>> > &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>> > Before restart, the COLVAR file contains ..<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>> > After restart, <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>> > 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>> > after restart,<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>> > Can anybody help me out how to restart the job?<br>> <br>> > Thanks.<br>> <br>> > Regards,<br>> > Sandeep<br>> <br>> > --<br>> > You received this message because you are subscribed to the Google Groups "cp2k" group.<br>
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> > For more options, visit this group athttp://<a href="http://groups.google.com/group/cp2k?hl=en">groups.google.com/group/cp2k?hl=en</a>.<br>