Mercurial > repos > chemteam > gmx_npt
annotate test-data/ions.mdp @ 1:93e39b0321c7 draft
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
author | chemteam |
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date | Thu, 04 Oct 2018 18:20:05 -0400 |
parents | 69ff679edefd |
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69ff679edefd
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
chemteam
parents:
diff
changeset
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1 ; ions.mdp - used as input into grompp to generate ions.tpr |
69ff679edefd
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
chemteam
parents:
diff
changeset
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2 ; Parameters describing what to do, when to stop and what to save |
69ff679edefd
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
chemteam
parents:
diff
changeset
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3 integrator = steep ; Algorithm (steep = steepest descent minimization) |
69ff679edefd
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
chemteam
parents:
diff
changeset
|
4 emtol = 1000.0 ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm |
69ff679edefd
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
chemteam
parents:
diff
changeset
|
5 emstep = 0.01 ; Energy step size |
69ff679edefd
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
chemteam
parents:
diff
changeset
|
6 nsteps = 50000 ; Maximum number of (minimization) steps to perform |
69ff679edefd
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
chemteam
parents:
diff
changeset
|
7 |
69ff679edefd
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
chemteam
parents:
diff
changeset
|
8 ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions |
69ff679edefd
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
chemteam
parents:
diff
changeset
|
9 nstlist = 1 ; Frequency to update the neighbor list and long range forces |
69ff679edefd
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
chemteam
parents:
diff
changeset
|
10 cutoff-scheme = Verlet |
69ff679edefd
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
chemteam
parents:
diff
changeset
|
11 ns_type = grid ; Method to determine neighbor list (simple, grid) |
69ff679edefd
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
chemteam
parents:
diff
changeset
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12 coulombtype = PME ; Treatment of long range electrostatic interactions |
69ff679edefd
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
chemteam
parents:
diff
changeset
|
13 rcoulomb = 1.0 ; Short-range electrostatic cut-off |
69ff679edefd
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
chemteam
parents:
diff
changeset
|
14 rvdw = 1.0 ; Short-range Van der Waals cut-off |
69ff679edefd
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
chemteam
parents:
diff
changeset
|
15 pbc = xyz ; Periodic Boundary Conditions (yes/no) |