<div dir="ltr">Hi Marcella,<div><br></div><div>Thank you, this is very helpful, makes a lot of sense. I will give both these options a try to see if I can make it work for my system as well as run my simulations longer.</div><div><br></div><div>Best,<br>Liam</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Thu, Oct 26, 2023 at 6:41 AM Marcella Iannuzzi <<a href="mailto:marci.akira@gmail.com">marci.akira@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div><br></div><div><br></div>Dear Liam<div><br></div><div>Metadynamics operates to alter the value of CV along the path of least energy.</div><div>The FES appears smoother and less steep when the molecules move apart instead of toward each other, which is logical. </div><div>Distances display quite a large range of variability and it may take a long time to explore the space defined by distances, even though the configurations at different distances relate to the same "chemical state", i.e., separated molecules. </div><div>Other variables, as coordination, may prove more effective, as the "separated molecules" state corresponds to a coordination of zero. After exploring this region of the space, it is expected that the algorithm will search for other regions of coordination greater than zero. </div><div>An alternative, approach would be to narrow the range of variability in distances by applying a restraining potential. </div><div><br></div><div>Regards</div><div>Marcella<br><br></div><div class="gmail_quote"><div dir="auto" class="gmail_attr">On Tuesday, October 24, 2023 at 5:18:21 PM UTC+2 Liam H wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">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-wrap"> </span>&END COLVAR<br><br> &COLVAR<br> &DISTANCE<br> ATOMS 2 16<br> &END DISTANCE<br><span style="white-space:pre-wrap"> </span>&END COLVAR<br><br><span style="white-space:pre-wrap"> </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></blockquote></div> <p></p> -- <br> You received this message because you are subscribed to the Google Groups "cp2k" group.<br> To unsubscribe from this group and stop receiving emails from it, send an email to <a href="mailto:cp2k+unsubscribe@googlegroups.com" target="_blank">cp2k+unsubscribe@googlegroups.com</a>.<br> To view this discussion on the web visit <a href="https://groups.google.com/d/msgid/cp2k/f7d22c0b-7217-4096-b222-9d6fbd6f5232n%40googlegroups.com?utm_medium=email&utm_source=footer" target="_blank">https://groups.google.com/d/msgid/cp2k/f7d22c0b-7217-4096-b222-9d6fbd6f5232n%40googlegroups.com</a>.<br> 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