exercises:2014_ethz_mmm:nacl_free_energy
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| exercise:nacl_free_energy [2014/05/28 16:34] – oschuett | exercises:2014_ethz_mmm:nacl_free_energy [2020/08/21 10:15] (current) – external edit 127.0.0.1 | ||
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| Line 2: | Line 2: | ||
| <note tip> | <note tip> | ||
| - | In this exercise you have to run many similar simulations. Try to automatize as much as possible. | + | * You' |
| + | * The first two task can be run directly on the login node, i.e. without using bsub. | ||
| + | * The third task should be run on 4 cores with '' | ||
| </ | </ | ||
| Line 32: | Line 34: | ||
| From these forces the free energy difference can be obtained via integration: | From these forces the free energy difference can be obtained via integration: | ||
| \begin{equation} | \begin{equation} | ||
| - | \Delta A = \int_a^b F(x)\, dx | + | \Delta A = -\int_a^b F(x)\, dx |
| \end{equation} | \end{equation} | ||
| A dissociation profile can be obtained by choosing the closest distance $d_{min}$ as lower integration-bound: | A dissociation profile can be obtained by choosing the closest distance $d_{min}$ as lower integration-bound: | ||
| \begin{equation} | \begin{equation} | ||
| - | A(d) = \int_{d_{min}}^d F(x)\, dx | + | A(d) = -\int_{d_{min}}^d F(x)\, dx |
| \end{equation} | \end{equation} | ||
| Line 44: | Line 46: | ||
| </ | </ | ||
| - | Compare the free-energy dissociation curve at 1K with the potential energy curve. What do you expect? What do you observer? | + | Compare the free-energy dissociation curve at 1K with the potential energy curve. What do you expect? What do you observe? |
| ===== 3. Task: Free energy curve of NaCl in water at 350K ===== | ===== 3. Task: Free energy curve of NaCl in water at 350K ===== | ||
| - | Take the solvated system from the [[exercise:nacl_md | first exercise]], add the constraint for a distance of 2.9 Å, and run 100.000 MD steps MD at 350K. Calculate | + | Take the solvated system from the [[nacl_md | first exercise]] |
| - | + | ||
| - | <note todo> | + | |
| - | Check convergence, | + | |
| - | </ | + | |
| ===== Required Files ===== | ===== Required Files ===== | ||
| Line 82: | Line 80: | ||
| EPSILON [kcalmol] | EPSILON [kcalmol] | ||
| SIGMA | SIGMA | ||
| + | RCUT [angstrom] 11.4 | ||
| + | &END LENNARD-JONES | ||
| + | & | ||
| + | atoms Na Na | ||
| + | EPSILON [kcalmol] | ||
| + | SIGMA | ||
| + | RCUT [angstrom] 11.4 | ||
| + | &END LENNARD-JONES | ||
| + | & | ||
| + | atoms Cl Cl | ||
| + | EPSILON [kcalmol] | ||
| + | SIGMA | ||
| RCUT [angstrom] 11.4 | RCUT [angstrom] 11.4 | ||
| &END LENNARD-JONES | &END LENNARD-JONES | ||
| Line 176: | Line 186: | ||
| < | < | ||
| # dist avg. Shake Lagrange multiplier | # dist avg. Shake Lagrange multiplier | ||
| - | 2.5 0.0896757 | + | |
| - | | + | 2.6 0.0469698 |
| - | | + | 2.7 0.0231717 |
| - | | + | 2.8 0.0100625 |
| - | | + | 2.9 <--- Take missing value from your trajectory |
| - | | + | 3.0 -0.000996937 |
| - | | + | 3.1 -0.00271078 |
| - | | + | 3.2 -0.00335324 |
| - | | + | 3.3 -0.00348111 |
| - | | + | 3.4 -0.00303697 |
| - | | + | 3.5 -0.00259636 |
| - | | + | 3.6 -0.00201541 |
| - | | + | 3.7 -0.00119027 |
| - | | + | 3.8 -0.000408723 |
| - | | + | 3.9 -8.19056e-05 |
| - | | + | 4.0 0.000972204 |
| - | | + | 4.1 0.00136578 |
| - | | + | 4.2 0.0016246 |
| - | | + | 4.3 0.00212447 |
| - | | + | 4.4 0.00199128 |
| - | | + | 4.5 0.00183284 |
| - | | + | 4.6 0.00188221 |
| - | | + | 4.7 0.00166909 |
| - | | + | 4.8 0.00137179 |
| - | | + | 4.9 0.00114308 |
| - | | + | 5.0 0.000671159 |
| - | | + | 5.1 0.000780625 |
| - | | + | 5.2 0.000556307 |
| - | | + | 5.3 0.000397211 |
| - | | + | 5.4 0.000237853 |
| - | | + | 5.5 0.000119549 |
| - | | + | 5.6 -0.000220194 |
| - | | + | 5.7 -0.000332539 |
| - | | + | 5.8 -0.000674227 |
| - | | + | 5.9 -0.00075852 |
| - | | + | 6.0 -0.00043128 |
| </ | </ | ||
exercises/2014_ethz_mmm/nacl_free_energy.1401294892.txt.gz · Last modified: 2020/08/21 10:14 (external edit)