exercises:2018_ethz_mmm:pmf
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Both sides previous revisionPrevious revision | Next revisionBoth sides next revision | ||
exercises:2018_ethz_mmm:pmf [2018/05/25 11:09] – dpasserone | exercises:2018_ethz_mmm:pmf [2018/05/25 11:13] – dpasserone | ||
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timestep 1.0 | timestep 1.0 | ||
# (4) NVT Dynamics | # (4) NVT Dynamics | ||
- | fix temp1 molecule nvt temp 300 300 100 | + | fix temp1 molecule nvt temp _TEMP_ _TEMP_ |
- | fix temp2 substrate nvt temp 300 300 100 | + | fix temp2 substrate nvt temp _TEMP_ _TEMP_ |
- | velocity | + | velocity |
fix PMF molecule recenter NULL _Y_ NULL | fix PMF molecule recenter NULL _Y_ NULL | ||
compute temp_molecule molecule temp | compute temp_molecule molecule temp | ||
Line 86: | Line 86: | ||
thermo_modify flush yes | thermo_modify flush yes | ||
thermo 50 | thermo 50 | ||
- | dump xyz all xyz 100000 | + | dump xyz all xyz 100000000 |
dump_modify xyz element C C H C N K Cl | dump_modify xyz element C C H C N K Cl | ||
dump coord all dcd 5000 trajectory.dcd | dump coord all dcd 5000 trajectory.dcd | ||
- | restart | + | restart |
run _NSTEPS_ | run _NSTEPS_ | ||
</ | </ | ||
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<note important> | <note important> | ||
- | - Edit the input file to run 50 picoseconds. | + | - Edit the input file to run 50 picoseconds, to write the restart at the end, to thermalize at the wished temperature. The length of the simulation is small to get converged averages, but the run will thus last a few minutes per distance |
- Now run the chain of simulations | - Now run the chain of simulations | ||
< | < |
exercises/2018_ethz_mmm/pmf.txt · Last modified: 2020/08/21 10:15 by 127.0.0.1