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 revision | ||
exercise:nacl_free_energy [2014/05/28 13:23] – oschuett | exercises:2014_ethz_mmm:nacl_free_energy [2020/08/21 10:15] (current) – external edit 127.0.0.1 | ||
---|---|---|---|
Line 1: | Line 1: | ||
====== 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) ===== | ||
Line 8: | Line 14: | ||
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 '' | ||
Line 22: | Line 28: | ||
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}' |
</ | </ | ||
Line 28: | 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 40: | 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 305K ===== | + | ===== 3. Task: Free energy curve of NaCl in water at 350K ===== |
- | - Check convergence, | + | 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. |
- | + | ||
- | <note tip> | + | |
- | Running many similar simulations is tedious. Try to automatize as much as possible. | + | |
- | </ | + | |
===== 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 113: | 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 134: | 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 147: | 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.1401283407.txt.gz · Last modified: 2020/08/21 10:14 (external edit)