exercises:2014_ethz_mmm:nacl_free_energy
Differences
This shows you the differences between two versions of the page.
Both sides previous revisionPrevious revisionNext revision | Previous revisionLast revisionBoth sides next revision | ||
exercise:nacl_free_energy [2014/05/28 12:25] – exercise:13_2 renamed to exercise:nacl_free_energy oschuett | exercise:2014_ethz_mmm:nacl_free_energy [2014/10/15 13:36] – oschuett | ||
---|---|---|---|
Line 1: | Line 1: | ||
- | ====== | + | ====== |
- | Plot a gas phase dissociation profile of NaCl based on potential energy using the input file '' | + | <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 | ||
+ | * The third task should be run on 4 cores with '' | ||
+ | </ | ||
- | Plot a gas phase dissociation profile of NaCl based on thermodynamic integration | + | ===== 1. Task: Potential energy curve (gas phase) ===== |
+ | Plot the gas phase dissociation profile of NaCl of the potential energy. For this you have to run the input file '' | ||
- | using the input file '' | ||
- | The constrained MD runs will produce | + | ===== 2. Task: Free energy curve at 1K (gas phase) ===== |
+ | 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 '' | ||
+ | |||
+ | Each constrained MD will produce | ||
< | < | ||
Shake Lagrangian Multipliers: | Shake Lagrangian Multipliers: | ||
Line 16: | Line 25: | ||
</ | </ | ||
- | For the thermodynamic integration | + | |
+ | From these files you can calculate | ||
< | < | ||
- | 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}' |
</ | </ | ||
- | < | + | The average Lagrange multiplier is the average force $F(x)$ required to constrain the atoms at the distance $x$. |
- | Running many similar simulations is tedious. Try to automatize as much as possible. | + | From these forces the free energy difference can be obtained via integration: |
+ | \begin{equation} | ||
+ | \Delta A = -\int_a^b F(x)\, dx | ||
+ | \end{equation} | ||
+ | |||
+ | A dissociation profile can be obtained by choosing the closest distance $d_{min}$ as lower integration-bound: | ||
+ | \begin{equation} | ||
+ | A(d) = -\int_{d_{min}}^d F(x)\, dx | ||
+ | \end{equation} | ||
+ | |||
+ | < | ||
+ | Make sure that you get the units right. The Largange multipliers are written in atomic units (Hartree/ | ||
</ | </ | ||
+ | |||
+ | 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 ===== | ||
+ | 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 ===== | ||
- | <code - motion.inp> | + | |
- | &MOTION | + | |
- | & | + | |
- | & | + | ==== Input file for NaCl in gasphase ==== |
- | 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> | ||
Line 87: | 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 108: | Line 113: | ||
Cl MYDIST 0.0 0.0 CLM | Cl MYDIST 0.0 0.0 CLM | ||
& | & | ||
+ | & | ||
+ | & | ||
+ | ATOMS 1 2 | ||
+ | &END DISTANCE | ||
+ | |||
+ | &END | ||
+ | & | ||
& | & | ||
CONNECTIVITY GENERATE | CONNECTIVITY GENERATE | ||
Line 121: | Line 133: | ||
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 | ||
+ | & | ||
+ | & | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | & | ||
+ | & | ||
+ | | ||
+ | | ||
+ | | ||
+ | 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.txt · Last modified: 2020/08/21 10:15 by 127.0.0.1