exercises:2014_ethz_mmm:nacl_free_energy
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exercise:nacl_free_energy [2014/05/28 16:06] – oschuett | exercises:2014_ethz_mmm:nacl_free_energy [2020/08/21 10:15] (current) – external edit 127.0.0.1 | ||
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====== Free Energy Profile of NaCl Dissociation====== | ====== Free Energy Profile of NaCl Dissociation====== | ||
+ | |||
+ | <note tip> | ||
+ | * You'll have to run many similar simulations. Try to automatize as much as possible. | ||
+ | * 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 '' | ||
+ | </ | ||
===== 1. Task: Potential energy curve (gas phase) ===== | ===== 1. Task: Potential energy curve (gas phase) ===== | ||
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Plot the gas phase dissociation profile of NaCl of the free energy at 1K. | Plot the gas phase dissociation profile of NaCl of the free energy at 1K. | ||
- | For this you have to run constrained MD simulations at 1K for a range of Na-Cl distances. You have to add the '' | + | For this you have to run constrained MD simulations at 1K for a range of Na-Cl distances. You have to add the '' |
Each constrained MD will produce a '' | Each constrained MD will produce a '' | ||
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From these files you can calculate the average Lagrange multiplier of the Shake-algorithm like this: | From these files you can calculate the average Lagrange multiplier of the Shake-algorithm like this: | ||
< | < | ||
- | grep Shake NACL-DIMER-XXX.LagrangeMultLog | awk '{c++ ; s=s+$4}END{print s/c}' | + | grep Shake NACL-XXX.LagrangeMultLog | awk '{c++ ; s=s+$4}END{print s/c}' |
</ | </ | ||
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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} | ||
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</ | </ | ||
- | 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]], the constraints | + | Take the solvated system from the [[nacl_md | first exercise]] |
+ | ===== Required Files ===== | ||
- | - Check convergence, | ||
- | < | ||
- | # dist avg. Shake Lagrange multiplier | ||
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- | </ | ||
- | <note tip> | ||
- | Running many similar simulations is tedious. Try to automatize as much as possible. | ||
- | </ | ||
- | ===== Required Files ===== | + | ==== Input file for NaCl in gasphase |
- | <code - motion.inp> | + | |
- | & | + | |
- | & | + | |
- | & | + | |
- | COLVAR 1 | + | |
- | INTERMOLECULAR | + | |
- | TARGET [angstrom] MYDIST | + | |
- | &END COLLECTIVE | + | |
- | & | + | |
- | COMMON_ITERATION_LEVELS 1 | + | |
- | &END | + | |
- | & | + | |
- | & | + | |
- | | + | |
- | | + | |
- | | + | |
- | | + | |
- | & | + | |
- | & | + | |
- | | + | |
- | | + | |
- | | + | |
- | MTS 2 | + | |
- | & | + | |
- | & | + | |
- | & | + | |
- | & | + | |
- | & | + | |
- | & | + | |
- | & | + | |
- | & | + | |
- | & | + | |
- | & | + | |
- | & | + | |
- | & | + | |
- | & | + | |
- | & | + | |
- | &END MOTION | + | |
- | </ | + | |
<code - NaCl_gasphase.inp> | <code - NaCl_gasphase.inp> | ||
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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 | ||
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Cl MYDIST 0.0 0.0 CLM | Cl MYDIST 0.0 0.0 CLM | ||
& | & | ||
+ | & | ||
+ | & | ||
+ | ATOMS 1 2 | ||
+ | &END DISTANCE | ||
+ | |||
+ | &END | ||
+ | & | ||
& | & | ||
CONNECTIVITY GENERATE | CONNECTIVITY GENERATE | ||
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RUN_TYPE ENERGY | RUN_TYPE ENERGY | ||
&END GLOBAL | &END GLOBAL | ||
+ | </ | ||
+ | ==== Motion section for constrained MD ==== | ||
+ | <code - motion.inp> | ||
+ | &MOTION | ||
+ | & | ||
+ | & | ||
+ | COLVAR 1 | ||
+ | INTERMOLECULAR | ||
+ | TARGET [angstrom] MYDIST | ||
+ | &END COLLECTIVE | ||
+ | & | ||
+ | COMMON_ITERATION_LEVELS 1 | ||
+ | &END | ||
+ | & | ||
+ | & | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | & | ||
+ | & | ||
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+ | | ||
+ | MTS 2 | ||
+ | & | ||
+ | & | ||
+ | & | ||
+ | & | ||
+ | & | ||
+ | & | ||
+ | & | ||
+ | & | ||
+ | & | ||
+ | & | ||
+ | & | ||
+ | &END | ||
+ | & | ||
+ | &END VELOCITIES | ||
+ | &FORCES OFF | ||
+ | &END FORCES | ||
+ | & | ||
+ | &END RESTART_HISTORY | ||
+ | & | ||
+ | &END RESTART | ||
+ | & | ||
+ | &END MOTION | ||
</ | </ | ||
+ | |||
+ | ==== Average Largange multiplier for NaCl in water at 350K (incomplete) ==== | ||
+ | < | ||
+ | # dist avg. Shake Lagrange multiplier | ||
+ | 2.5 | ||
+ | 2.6 | ||
+ | 2.7 | ||
+ | 2.8 | ||
+ | 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 | ||
+ | 4.1 | ||
+ | 4.2 | ||
+ | 4.3 | ||
+ | 4.4 | ||
+ | 4.5 | ||
+ | 4.6 | ||
+ | 4.7 | ||
+ | 4.8 | ||
+ | 4.9 | ||
+ | 5.0 | ||
+ | 5.1 | ||
+ | 5.2 | ||
+ | 5.3 | ||
+ | 5.4 | ||
+ | 5.5 | ||
+ | 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.1401293170.txt.gz · Last modified: 2020/08/21 10:14 (external edit)