Table of Contents
Free Energy Profile of NaCl Dissociation
- 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
bsub -n 4.
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 NaCl_gasphase.inp at a range of Na-Cl distances.
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 MOTION-section provided below to the NaCl_gasphase.inp and change the RUN_TYPE.
Each constrained MD will produce a .LagrangeMultLog-files, which look like this:
Shake Lagrangian Multipliers: -0.054769270 Rattle Lagrangian Multipliers: -0.020937479 Shake Lagrangian Multipliers: -0.020937479 Rattle Lagrangian Multipliers: -0.020937479 ...
From these files you can calculate the average Lagrange multiplier of the Shake-algorithm like this:
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 $x$. 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}
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 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
Input file for NaCl in gasphase
- NaCl_gasphase.inp
&FORCE_EVAL METHOD FIST &MM &FORCEFIELD &SPLINE EPS_SPLINE 1.0E-8 EMAX_SPLINE 300000.0 &END &CHARGE ATOM Na CHARGE 1.0 &END CHARGE &CHARGE ATOM Cl CHARGE -1.0 &END CHARGE &NONBONDED &LENNARD-JONES atoms Na Cl EPSILON [kcalmol] .0838 SIGMA [angstrom] 3.63 RCUT [angstrom] 11.4 &END LENNARD-JONES &LENNARD-JONES atoms Na Na EPSILON [kcalmol] 0.0469 SIGMA [angstrom] 2.7275 RCUT [angstrom] 11.4 &END LENNARD-JONES &LENNARD-JONES atoms Cl Cl EPSILON [kcalmol] 0.150 SIGMA [angstrom] 4.54 RCUT [angstrom] 11.4 &END LENNARD-JONES &END NONBONDED &END FORCEFIELD &POISSON &EWALD EWALD_TYPE spme ALPHA .3 GMAX 12 O_SPLINE 6 &END EWALD &END POISSON &END MM &SUBSYS &CELL ABC 12.4138 12.4138 12.4138 &END CELL &COORD Na 0.0 0.0 0.0 NAP Cl MYDIST 0.0 0.0 CLM &END COORD &COLVAR &DISTANCE ATOMS 1 2 &END DISTANCE &PRINT &END &END COLVAR &TOPOLOGY CONNECTIVITY GENERATE &GENERATE BONDLENGTH_MAX 7 &END &END &END SUBSYS &END FORCE_EVAL &GLOBAL PROJECT NACL-MYDIST RUN_TYPE ENERGY &END GLOBAL
Motion section for constrained MD
- motion.inp
&MOTION &CONSTRAINT &COLLECTIVE COLVAR 1 INTERMOLECULAR TARGET [angstrom] MYDIST &END COLLECTIVE &LAGRANGE_MULTIPLIERS COMMON_ITERATION_LEVELS 1 &END &END CONSTRAINT &MD ENSEMBLE NVT TIMESTEP 0.5 STEPS 100 TEMPERATURE 1 &THERMOSTAT &NOSE LENGTH 3 YOSHIDA 3 TIMECON 1000 MTS 2 &END NOSE &END &PRINT &ENERGY OFF &END ENERGY &PROGRAM_RUN_INFO OFF &END PROGRAM_RUN_INFO &END PRINT &END MD &PRINT &TRAJECTORY OFF &END &VELOCITIES OFF &END VELOCITIES &FORCES OFF &END FORCES &RESTART_HISTORY OFF &END RESTART_HISTORY &RESTART OFF &END RESTART &END PRINT &END MOTION
Average Largange multiplier for NaCl in water at 350K (incomplete)
# dist avg. Shake Lagrange multiplier 2.5 0.0896372 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