exercises:2014_ethz_mmm:nacl_free_energy
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| exercise:nacl_free_energy [2014/05/29 11:57] – [3. Task: Free energy curve of NaCl in water at 350K] vondele | 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 48: | Line 50: | ||
| ===== 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]] and add the constraint for a distance of 2.9 Å. Then run 100.000 MD steps MD at 350K. From the MD output calculate the average Largange multiplier. As a check for convergence you can divide the trajectory into two parts and calculate the average for each part separately. Once you are convinced of the result you can use it to complete the table given below. From the complete table calculate the free energy dissociation profile via numerical integration. | + | Take the solvated system from the [[nacl_md | first exercise]] and add the constraint for a distance of 2.9 Å. Then run 100.000 MD steps MD at 350K. From the MD output calculate the average Largange multiplier. As a check for convergence you can divide the trajectory into two parts and calculate the average for each part separately. Once you are convinced of the result you can use it to complete the table given below. From the complete table calculate the free energy dissociation profile via numerical integration. |
| ===== Required Files ===== | ===== Required Files ===== | ||
| Line 78: | 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 172: | 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.1401364675.txt.gz · Last modified: 2020/08/21 10:14 (external edit)