Mercurial > repos > chemteam > gmx_setup
comparison test-data/minim.mdp @ 0:644ca8dfdf28 draft
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
| author | chemteam |
|---|---|
| date | Thu, 04 Oct 2018 17:39:10 -0400 |
| parents | |
| children | 4da9ee404eab |
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| -1:000000000000 | 0:644ca8dfdf28 |
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| 1 ; minim.mdp - used as input into grompp to generate em.tpr | |
| 2 integrator = steep ; Algorithm (steep = steepest descent minimization) | |
| 3 emtol = 1000.0 ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm | |
| 4 emstep = 0.01 ; Energy step size | |
| 5 nsteps = 50000 ; Maximum number of (minimization) steps to perform | |
| 6 | |
| 7 ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions | |
| 8 nstlist = 1 ; Frequency to update the neighbor list and long range forces | |
| 9 cutoff-scheme = Verlet | |
| 10 ns_type = grid ; Method to determine neighbor list (simple, grid) | |
| 11 coulombtype = PME ; Treatment of long range electrostatic interactions | |
| 12 rcoulomb = 1.0 ; Short-range electrostatic cut-off | |
| 13 rvdw = 1.0 ; Short-range Van der Waals cut-off | |
| 14 pbc = xyz ; Periodic Boundary Conditions (yes/no) |