GROMACS 4.6 example: Direct ethanol solvation free energy

From AlchemistryWiki
Jump to: navigation, search



Setting up the calculation with Gromacs

This tutorial assumes knowledge of Gromacs. Make sure you actually know how to use Gromacs first.

There are nine intermediate states defined to perform the calculation of the absolute solvation free energy of ethanol (also known as the chemical potential at infinite dilution). You will need to run nine different simulations. The will use the SAME .gro file (ethanol.gro), the SAME .top file, (ethanol.top) and nine different .mdp (ethanol.mdp) files. But the .mdp files will only be different by one line,

  init-lambda-state = X

Where X is 0 through 8, inclusive, because there are 9 states.

Running the calculation with Gromacs

Run grompp and mdrun as normal. Specifically:

  grompp -f ethanol.X.mdp -c ethanol.gro -p ethanol.top -o ethanol.X.tpr -maxwarn 4

There may be some warnings, and you'll need to override, hence -maxwarn. X runs from 0 to 8.

The number of threads can be anything you want (less than the number run on the cluster) If running on the cluster, you will also want to set the -nopin flag. If you don't set the dhdl file independently, it will be saved to ethanol.X.xvg, and might get written over accidentally if you run g_energy. X again runs 0-8

    mdrun -nt 1 -deffnm ethanol.X -dhdl ethanol.X.dhdl.xvg

Strictly, you will only need the dhdl files, but looking at the others output files can be useful to determine

Analyze the calculation with Gromacs

After you have generated the dhdl files, you can then analyze them using pymbar with the dhdl output.

You will need to install [pymbar] and [pymbar-examples] alchemical-gromacs.py will be in the pymbar-examples/alchemical-free-energy directory. Go to the web page and 'git clone' the files:

  git clone https://github.com/choderalab/pymbar.git 
  git clone https://github.com/choderalab/pymbar-examples.git

The invocation of the analysis code is:

  python alchemical-gromacs.py -f directory/prefix -t 300 -p 1 -n 2500 -v  > outputfile

'-t' is temperature, '-p' is pressure, '-f' is (prefix of the files, including directory if alchemical-gromacs.py is not called from the directory in which the files are stored), and '-v' is verbose output (not required, but helpful to understand!) Instructions are also in the pymbar-examples directory.

It will use all files it finds with the given prefix, and it will assume they are numbered in order. If your dhdl files are named with an ethanol. prefix then you should make sure that they are in their own directory before calling alchemical-gromacs.py so that alchemical-gromacs.py only acts on the dhdl files and not other ethanol. files in the directory. We omit the first 500 ps (0.2 ps per sample) for equilibration (likely overkill for this problem, but better safe than sorry).

You may see the following warnings:

  Warning on use of the timeseries module: If the inherent timescales of the system are long compared to those being analyzed, 
  this statistical inefficiency may be an underestimate.  The estimate presumes the use of many statistically independent samples
  Tests should be performed to assess whether this condition is satisfied.   Be cautious in the interpretation of the data

This is a standard warning -- the correlation time code will be an underestimate if there are correlation times that are long with respect to the simulation time. In this case, there aren't. With proteins, there probably are.

  /Users/mrshirts/work/papers/MBARFORDUMMIES/pymbar/trunk/pymbar/pymbar.py:308: RuntimeWarning: overflow encountered in exp
   log_f_R = - max_arg_R - numpy.log( numpy.exp(-max_arg_R) + numpy.exp(exp_arg_R - max_arg_R) ) - w_R
   /Users/mrshirts/work/papers/MBARFORDUMMIES/pymbar/trunk/pymbar/pymbar.py:494: RuntimeWarning: overflow encountered in exp
    fR =  1/(1+numpy.exp(w_R - C))

These warnings can pop up because we are using BAR initialization in the algorithm, which is a bit faster (not much). It will default to zeros, which is fine. As long as the MBAR calculation converges OK, these warnings can be ignored.

Understanding the analysis

Let's look at the output file:

 The number of files read in for processing is:  9
 output is verbose
 Reading metadata from solvation_direct/outputs/dhdls/ethanol_direct_few.0.dhdl.xvg...
 Done reading metadata from solvation_direct/outputs/dhdls/ethanol_direct_few.0.dhdl.xvg...
 Reading solvation_direct/outputs/dhdls/ethanol_direct_few.0.dhdl.xvg...
 Reading solvation_direct/outputs/dhdls/ethanol_direct_few.1.dhdl.xvg...
 Reading solvation_direct/outputs/dhdls/ethanol_direct_few.2.dhdl.xvg...
 Reading solvation_direct/outputs/dhdls/ethanol_direct_few.3.dhdl.xvg...  
 Reading solvation_direct/outputs/dhdls/ethanol_direct_few.4.dhdl.xvg...
 Reading solvation_direct/outputs/dhdls/ethanol_direct_few.5.dhdl.xvg...
 Reading solvation_direct/outputs/dhdls/ethanol_direct_few.6.dhdl.xvg...
 Reading solvation_direct/outputs/dhdls/ethanol_direct_few.7.dhdl.xvg...
 Reading solvation_direct/outputs/dhdls/ethanol_direct_few.8.dhdl.xvg...

All standard stuff saying what it's doing. The next part is important. pymbar determines how many of the samples are statistically uncorrelated, and only uses every [math]1/\tau[/math] samples.

  Now computing correlation times
  Correlation times:
  [ 1.13024145  1.53302243  1.43612724  1.08803448  1.55534344  1.37338905 1.40559608  1.08837468  1.083193  ]
  number of uncorrelated samples:
  [24331 17939 19149 25275 17681 20024 19565 25267 25388]

The next part is initalization information. We use the (faster, ignores information Bennett's acceptance ratio to get a quick estimate of the free energies between states, and refine it with multistate Bennett's acceptance ratio. For simple calculations, probably overkill.

 relative_change =        1.000
 iteration     0 : DeltaF =            4.609
 relative_change =        0.000
 iteration     1 : DeltaF =            4.609
 relative_change =        0.000
 Convergence achieved.
 Converged to tolerance of 8.439389e-13 in 2 iterations (5 function evaluations)
 DeltaF =    4.609 +-    0.007

Goes on like that for a while. Then we actually start the MBAR calculation. Some diagnostic information at the beginning.

  Computing free energy differences...
  Using embedded C++ helper code.
  K = 9, L = 9, N_max = 27500, total samples = 194619
  There are 9 states with samples.
  N_k =
  [24331 17939 19149 25275 17681 20024 19565 25267 25388]
  Initial dimensionless free energies with method BAR

This is starting iteration. These f_k's are free energies times [math]\beta[/math], so they are dimensionless. Don't get confused between these values and the final values for the free energies of each state.

  f_k =
  [  0.           4.60854858   8.63821596  10.52813716  12.39909138
    13.90581448  14.60066295  12.653474     7.08947627]
  Determining dimensionless free energies by Newton-Raphson iteration.
  self consistent iteration gradient norm is     274.37, Newton-Raphson gradient norm is   0.001627
  Choosing self-consistent iteration on iteration 0
  current f_k for states with samples =
  [  0.           4.60851302   8.63587897  10.52784259  12.39754897
    13.90747094  14.60015956  12.65309141   7.08891004]
  relative max_delta = 1.600662e-04
  self consistent iteration gradient norm is     61.179, Newton-Raphson gradient norm is 1.0307e-05
  Choosing self-consistent iteration for lower gradient on iteration 1
  current f_k for states with samples =
  [  0.           4.60810077   8.63487764  10.52740478  12.39729092
    13.90745661  14.60018318  12.65278436   7.08849961]
  relative max_delta = 6.858353e-05
  self consistent iteration gradient norm is     15.488, Newton-Raphson gradient norm is 4.3297e-07
  Newton-Raphson used on iteration 2

And it goes on like that for a while. It switched to Newton-Raphson once it appears to be converging. This might take 1 step, it might take 5-10 steps. Once it switches to Newton-Raphson, it will go very quickly.

Soon (should just be a few seconds!) we get:

  Converged to tolerance of 3.175483e-14 in 5 iterations.
  Of 5 iterations, 3 were Newton-Raphson iterations and 2 were self-consistent iterations
  Recomputing all free energies and log weights for storage
  Final dimensionless free energies
  f_k =
  [  0.           4.60763423   8.63398184  10.52688519  12.39691766
    13.9073167   14.6002695   12.65255384   7.08801044]
  MBAR initialization complete.

Now let's get to the the results:

First, it prints "Deltaf_ij". These are the values of [math]\beta\Delta G_{ij}[/math]. It's a 9x9 matrix, because there are 9 states. The diagonal is zero, because the free energy difference between a state and itself is zero.

 Deltaf_ij:
 [[  0.           4.60763423   8.63398184  10.52688519  12.39691766
    13.9073167   14.6002695   12.65255384   7.08801044]
  [ -4.60763423   0.           4.02634761   5.91925096   7.78928344
     9.29968247   9.99263527   8.04491961   2.48037622]

Next, "dDeltaf_ij" the uncertainties in Deltaf_ij

 dDeltaf_ij:
 [[ 0.          0.00647308  0.01354042  0.01840233  0.0185153   0.01912802
    0.02082696  0.02560051  0.0281657 ]
  [ 0.00647308  0.          0.00916897  0.01537218  0.01550672  0.01623309
    0.0182042   0.02351631  0.02628569]

Finally, the full results. Six different methods to compare! The rows only run from 0 to 7, because there are only 8 free energy DIFFERENCES -- 0 to 1, 1 to 2, etc.

         TI (kJ/mol)   TI-CUBIC (kJ/mol)       DEXP (kJ/mol)       IEXP (kJ/mol)        BAR (kJ/mol)       MBAR (kJ/mol)
     0:    11.546 +-  0.016   11.516 +-  0.017   11.475 +-  0.031   11.588 +-  0.041   11.498 +-  0.017   11.496 +-  0.016
     1:    10.326 +-  0.023   10.071 +-  0.026   10.085 +-  0.057   10.009 +-  0.088   10.054 +-  0.024   10.046 +-  0.023
     2:     5.416 +-  0.027    4.706 +-  0.040    4.688 +-  0.106    4.961 +-  0.296    4.715 +-  0.027    4.723 +-  0.022
     3:     4.716 +-  0.015    4.751 +-  0.015    4.922 +-  0.049    4.665 +-  0.011    4.668 +-  0.010    4.666 +-  0.007
     4:     3.679 +-  0.012    3.686 +-  0.013    3.811 +-  0.029    3.746 +-  0.013    3.759 +-  0.011    3.768 +-  0.009
     5:     1.419 +-  0.017    1.965 +-  0.020    1.604 +-  0.170    1.759 +-  0.022    1.734 +-  0.016    1.729 +-  0.015
     6:    -5.418 +-  0.023   -5.320 +-  0.026   -5.115 +-  0.207   -4.947 +-  0.062   -4.858 +-  0.031   -4.859 +-  0.031
     7:   -13.178 +-  0.021  -13.654 +-  0.025  -13.911 +-  0.048  -13.676 +-  0.169  -13.882 +-  0.020  -13.883 +-  0.020
 ------------------- ------------------- ------------------- ------------------- ------------------- -------------------
 TOTAL:    18.505 +-  0.186   17.721 +-  0.198   17.559 +-  0.305   18.104 +-  0.361   17.688 +-  0.059   17.684 +-  0.070


Things to note: with 9 states, TI is not so good; it's about 1 kJ/mol away from the other values. If we use cubic interpolation to integrate, we improve the agreement with the other algorithms.

Exponential averaging in both directions, insertion and deletion (EXP and DEXP) are not that far off for this example, but the uncertainties are fairly large.

The values for BAR and MBAR are very close! But the uncertainty estimate of BAR is lower. it SEEMS like BAR is better, but that is actually because the BAR estimate is too low. If you ran the experiment lots of times, and computed the sample error you would get a result which is closer to 0.07 than 0.059. This is a known problem with BAR. The estimate of the pairwise differences (0-1, 1-2, 2-3) are all accurate, but the SUM is inaccurate, because the 0->1 and 1->2 calculations both share the same data set, data set 1.

MBAR is generally the lowest variance estimate for a given amount of sampling. In some special cases, TI can get lower, and is frequently almost as good IF enough intermediate states are included. BAR can be almost as good as MBAR, but the uncertainty estimate for the full calculation can frequently be too low.

These are very accurate calculations (in the case of MBAR). Note that they are correct to within 0.07 kJ/mol, which is 0.016 kcal/mol. This free energy can probably only be computed to within 0.05 kcal/mol experimentally.

Hamilton replica exchange

The same calculations can be run with Hamiltonian replica exchange. No changes are required for system preparation or analysis: only running mdrun. Getting this to run will very much depend on your cluster setup -- make sure you can get replica exchange working on your own cluster. But once it does work, you can run all the .mdp's with:

 mpiexec -np $NP  mdrun_mpi_d -defnm -multi 9 -replex 1000 -nex 100000 -deffnm ethanol. -dhdl ethanol.dhdl.

$NP should be a multiple of 9. It uses the "multiple swap" replica exchange formalism, which involves more movement between alchemical states. '-nex' indicates how many swaps to perform. -replex indicates how frequently (in units of steps) to perform exchanges. 1000 is pretty good for Hamiltonian replica exchange; shorter times means more mixing, and thus more sampling. There are potential issues if the velocities do not decorrelate between exchanges, because you could get velocities that cause a collision after a switched state, or that make the virial too big and explode pressure control dynamics. But any frequency longer than this correlation time should be fine.