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Table of Contents
Free Energy Profile of NaCl Dissociation
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-DIMER-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 observer?
3. Task: Free energy curve of NaCl in water at 350K
Take the solvated system from the first exercise, the constraints for a distance of 2.9 Å, and run MD again at 350K.
- Check convergence, running average, binning,…
# dist avg. Shake Lagrange multiplier 2.5 0.0896757 2.6 0.0471343 2.7 0.023305 2.8 0.0102343 2.9 <--- Take missing value from your trajectory 3.0 -0.000906449 3.1 -0.00284901 3.2 -0.00318466 3.3 -0.00325302 3.4 -0.00318047 3.5 -0.0027712 3.6 -0.00179401 3.7 -0.00143999 3.8 -0.000680095 3.9 0.000462241 4.0 0.000622342 4.1 0.00129275 4.2 0.00192298 4.3 0.00209414 4.4 0.00228705 4.5 0.00183497 4.6 0.00180152 4.7 0.00149531 4.8 0.00151825 4.9 0.00102442 5.0 0.000957486 5.1 0.000638038 5.2 0.000817498 5.3 0.000351418 5.4 0.000217036 5.5 3.14625e-05 5.6 3.12049e-05 5.7 -0.000479905 5.8 -0.000811917 5.9 -0.000666426 6.0 -0.000867775
Required Files
- motion.inp
&MOTION &CONSTRAINT &COLLECTIVE COLVAR 1 INTERMOLECULAR TARGET [angstrom] MYDIST &END COLLECTIVE &LAGRANGE_MULTIPLIERS COMMON_ITERATION_LEVELS 1 &END &END CONSTRAINT &MD ENSEMBLE NVE TIMESTEP 0.5 STEPS 100 TEMPERATURE 1 &THERMOSTAT &NOSE LENGTH 3 YOSHIDA 3 TIMECON 1000 MTS 2 &END NOSE &END THERMOSTAT &PRINT &TRAJECTORY OFF &END TRAJECTORY &VELOCITIES OFF &END VELOCITIES &FORCES OFF &END FORCES &RESTART_HISTORY OFF &END RESTART_HISTORY &RESTART OFF &END RESTART &END PRINT &END MOTION
- 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 &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 &TOPOLOGY CONNECTIVITY GENERATE &GENERATE BONDLENGTH_MAX 7 &END &END &END SUBSYS &END FORCE_EVAL &GLOBAL PROJECT NACL-MYDIST RUN_TYPE ENERGY &END GLOBAL