Hello,<div><br /></div><div>So I have a kind of general question, normally when I run metadynamics simulations, unimolecular the systems where a bond needs to be broken works easily with the bond distance CV.</div><div>But in the reverse case, a bimolecular system where bias needs to be added to make a bond form, or even a unimolecular system with flexible chains that need to cyclize, these systems tend to get get further and further apart instead of closer together..</div><div><br /></div><div>Does anyone have any tips on how to remedy this? This is an example of my input parameters (minus DFT and print sections), This is a unimolecular acyclic system that I am attempting to show cyclization in metadynamics. I ran only 10 000 steps so I could do more but it did not seem to make any progress.. the CVs don't really change at all</div><div><br /></div><div>Thank you,<br />Liam</div><div><br /></div><div>&GLOBAL<br /> PROJECT TS-1<br /> PRINT_LEVEL LOW<br /> RUN_TYPE MD<br />&END GLOBAL<br /><br />&FORCE_EVAL<br /> METHOD Quickstep<br /> &SUBSYS<br /> &CELL<br /> A 16.30464600 0.00000000 0.00000000<br /> B 0.00000000 16.90186000 0.00000000<br /> C 0.00000000 0.00000000 17.81548400<br /> PERIODIC XYZ #Direction(s) of applied PBC (geometry aspect)<br /> &END CELL<br /> &COORD<br /> C 1.05566000 0.66730000 -0.06403000<br /> C 1.16646000 -0.73817000 -0.01172000<br /> C 2.41800000 -1.28561000 0.31373000<br /> C 3.52794000 -0.48197000 0.56970000<br /> C 3.41209000 0.90158000 0.47292000<br /> C 2.18170000 1.46806000 0.15045000<br /> C -0.23374000 1.36196000 -0.37069000<br /> C -0.39935000 1.82258000 -1.68125000<br /> C -1.55390000 2.49392000 -2.07260000<br /> C -2.57130000 2.71290000 -1.14716000<br /> C -2.42186000 2.25411000 0.15599000<br /> C -1.25880000 1.58006000 0.58740000<br /> B -1.19524000 1.14740000 2.08650000<br /> Br 0.40816000 0.79973000 3.07109000<br /> Br -2.82356000 0.97103000 3.10636000<br /> Si -0.22795000 -1.94672000 -0.40552000<br /> C 0.41691000 -3.70245000 -0.32700000<br /> C -1.77233000 -1.79184000 0.63917000<br /> Br -0.85948000 -1.61419000 -2.55308000<br /> H 2.53894000 -2.36934000 0.36673000<br /> H 4.48380000 -0.93949000 0.82873000<br /> H 4.27648000 1.54227000 0.65408000<br /> H 2.07625000 2.55335000 0.09152000<br /> H 0.39256000 1.62706000 -2.40625000<br /> H -1.65976000 2.83803000 -3.10259000<br /> H -3.48256000 3.23620000 -1.43897000<br /> H -3.22803000 2.42901000 0.86879000<br /> H -0.38316000 -4.39064000 -0.63509000<br /> H 1.27092000 -3.84940000 -1.00275000<br /> H 0.72280000 -3.96581000 0.69732000<br /> H -2.41046000 -2.66949000 0.45752000<br /> H -2.35096000 -0.89299000 0.39003000<br /> H -1.51622000 -1.76845000 1.71066000<br /> &END COORD<br /><br /> &COLVAR<br /> &DISTANCE<br /> ATOMS 2 13<br /> &END DISTANCE<br /><span style="white-space: pre;"> </span>&END COLVAR<br /><br /> &COLVAR<br /> &DISTANCE<br /> ATOMS 2 16<br /> &END DISTANCE<br /><span style="white-space: pre;"> </span>&END COLVAR<br /><br /><span style="white-space: pre;"> </span><br /><br /># &VELOCITY #inital velocity<br /># &END VELOCITY<br /> &KIND C <br /> ELEMENT C <br /> BASIS_SET DZVP-MOLOPT-SR-GTH-q4<br /> POTENTIAL GTH-PBE<br /> &END KIND<br /> &KIND Si <br /> ELEMENT Si<br /> BASIS_SET DZVP-MOLOPT-SR-GTH-q4<br /> POTENTIAL GTH-PBE<br /> &END KIND<br /> &KIND Br <br /> ELEMENT Br<br /> BASIS_SET DZVP-MOLOPT-SR-GTH-q7<br /> POTENTIAL GTH-PBE<br /> &END KIND<br /> &KIND B <br /> ELEMENT B <br /> BASIS_SET DZVP-MOLOPT-SR-GTH-q3<br /> POTENTIAL GTH-PBE<br /> &END KIND<br /> &KIND H <br /> ELEMENT H <br /> BASIS_SET DZVP-MOLOPT-SR-GTH-q1<br /> POTENTIAL GTH-PBE<br /> &END KIND<br /> &END SUBSYS<br /><br />&MOTION<br /> &MD<br /> ENSEMBLE NVE<br /> STEPS 10000 #Number of steps to run<br /> TIMESTEP 0.5 #Step size in fs<br /> TEMPERATURE 400.0 #Initial and maintained temperature (K)<br /> ANGVEL_ZERO T #Eliminate overall rotation component from initial velocity<br /> &PRINT<br /> &PROGRAM_RUN_INFO<br /> &EACH<br /> MD 1 #Output frequency of MD information, 0 means never<br /> &END EACH<br /> &END PROGRAM_RUN_INFO<br /> &END PRINT<br /> &END MD<br /> &FREE_ENERGY<br /> &METADYN<br /> DO_HILLS <br /> NT_HILLS 50<br /> WW 3.0e-3<br /> TEMPERATURE 400<br /> TEMP_TOL 10.0<br /> WELL_TEMPERED<br /> DELTA_T 6000<br /> COLVAR_AVG_TEMPERATURE_RESTART 400<br /><br /> &METAVAR<br /> SCALE 0.2<br /> COLVAR 1<br /> &END METAVAR<br /><br /> &METAVAR<br /> SCALE 0.2<br /> COLVAR 2<br /> &END METAVAR<br /><br /> &PRINT<br /> &COLVAR<br /> COMMON_ITERATION_LEVELS 3<br /> &EACH<br /> MD 1<br /> &END<br /> &END<br /> &HILLS<br /> COMMON_ITERATION_LEVELS 3<br /> &EACH<br /> MD 1<br /> &END<br /> &END<br /> &END<br /> &END METADYN<br /> &END<br /><br /> &PRINT<br /> &TRAJECTORY<br /> &EACH<br /> MD 1 #Output frequency of coordinates, 0 means never<br /> &END EACH<br /> FORMAT xyz<br /> &END TRAJECTORY<br /> &VELOCITIES<br /> &EACH<br /> MD 0 #Output frequency of velocities, 0 means never<br /> &END EACH<br /> &END VELOCITIES<br /> &FORCES<br /> &EACH<br /> MD 0 #Output frequency of forces, 0 means never<br /> &END EACH<br /> &END FORCES<br /> &RESTART<br /> BACKUP_COPIES 0 #Maximum number of backing up restart file, 0 means never<br /> &EACH<br /> MD 1 #Frequency of updating last restart file, 0 means never<br /> &END EACH<br /> &END RESTART<br /> &RESTART_HISTORY OFF <br /> &END RESTART_HISTORY<br /> &END PRINT<br />&END MOTION<br /></div>
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