| energy: ENERGY equals the potential energy of GROMACS at every step, on 1 and 2 ranks |
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| pull: a RESTRAINT on the distance of two water oxygens acts as the GROMACS pull code: same positions over 20 steps, forces at step 0, and virial every 5 steps (the virial is computed on those steps only) |
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| pull-dd: as pull, on 2 ranks |
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| pull-energy: as pull, with ENERGY in the PLUMED input (PLUMED then runs when the energy is complete) |
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| pull-mts: as pull, with multiple time stepping and ENERGY needed on the slow steps |
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| mts-fast-step: with multiple time stepping, mdrun stops with an error if PLUMED needs the energy on a fast step |
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| vsite: a RESTRAINT between two virtual sites (TIP4P M sites) acts the same with and without ENERGY in the PLUMED input (with ENERGY, PLUMED runs after GROMACS spread the forces on the virtual sites), on 1 and 2 ranks |
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| energy-bias: a bias s*ENERGY multiplies all the forces by 1+s, also with virtual sites |
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| energy-bias-dd: with a bias on ENERGY, the virial is the same on 1, 2 and 3 ranks |
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| em: energy minimization with a restraint: the same steps on 1 and 2 ranks, and with and without ENERGY (restraints between two oxygens and between two virtual sites) |
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| data: PLUMED gets the positions, box, masses, charges and time of GROMACS |
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| checkpoint: PLUMED writes its state (OPES STATE_WFILE with STORE_STATES) at the steps where GROMACS writes a checkpoint, on 1 and 2 ranks |
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| committor: COMMITTOR stops mdrun soon after committing, with a final checkpoint, on 1 and 2 ranks |
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| committor-walkers: with two simulations (-multidir), all of them stop when one commits |
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| rerun: a rerun of a trajectory gives the CVs that PLUMED computed in the run, on 1 and 2 ranks; a stop request (COMMITTOR) ends the rerun |
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| hrex: -hrex with two identical replicas: the PLUMED energy difference is 0 (1 and 2 ranks per replica), and PLUMED does not calculate again on the exchange steps (one COLVAR line per step, the expected hills) |
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| shells: shell (polarizable) particles: PLUMED is applied once per step, also in a rerun, and mdrun warns when PLUMED needs the energy, which is the one before the shells are relaxed (or mdrun refuses shells) |
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| expanded: expanded ensemble: PLUMED’s lambda is the lambda state of GROMACS; with lmc-stats other than ‘no’, GROMACS still updates the weights |
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| md-vv: md-vv runs with PLUMED (the legacy patches use the legacy simulator, which supports it) |
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| replex-nex: replica exchange with -nex, which ignores the PLUMED bias, is refused |
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| replex-bias: temperature replica exchange with a PLUMED bias: the legacy patches add the bias to the exchange criterion; the native module refuses it with a clear error |
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| gpu-buffer-ops: with nonbonded and PME on the GPU, the restraint acts the same with GPU force buffer operations |
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