66
umbrella1.tpr
umbrella2.tpr
…
umbrella50.tpr
Name this file tpr-files.dat.
2. Create another text file where all the force files will be noted in
ascending order:
umbrella1_pullf.xvg
umbrella2_pullf.xvg
…
umbrella50_pullf.xvg
and name this file pullf-files.dat.
In order to conduct the WHAM analysis use the following terminal command:
gmx_d wham -it tpr-files.dat -if pullf-files.
dat -o profile.xvg –hist histo.xvg -unit
kCal -bs-method b-his -nBootstrap 100 -bsres
The –it and –if options provide the WHAM module with the tpr
and force files, respectively. The output option (−o) provides the output file profile.xvg which contains the PMF plot for the process under
study, while the –hist provides the histo.xvg file which contains the
histograms of the process. The histogram analysis ensures that the
sampling around a reaction coordinate is adequate. An indication of
adequate sampling is a good overlap between the histograms of each
consequent window, as illustrated in Fig. 13. The –unit option defines
the unit for the energy value (in this case, the chemically relevant unit
of kcal/mol is preferred). The –bs method option is used in order to
define the error analysis method. In this case, we provide the keyword b-his in order to use the Bayesian bootstrap method for our
error analysis. With this method, complete histograms are considered
as independent data points, and the bootstrap is carried out by assigning random weights to the histograms. The –nBootstrap provides the
number of bootstraps to be used for the error analysis, in this case
100. For further details on the statistical analysis, please refer to reference [7]. The –bsres option provides the output of the Bootstrap
analysis which is a .xvg file containing the PMF plot along with the
standard deviations in energy.
Following these steps, the umbrella sampling simulation will
be completed. The results for CC:2-HP-B-CD complex are presented and briefly discussed in Fig. 14.
3.6.2 Run the WHAM
Analysis
Sofia Kiriakidi and Thomas Mavromoustakos
umbrella1.tpr
umbrella2.tpr
…
umbrella50.tpr
Name this file tpr-files.dat.
2. Create another text file where all the force files will be noted in
ascending order:
umbrella1_pullf.xvg
umbrella2_pullf.xvg
…
umbrella50_pullf.xvg
and name this file pullf-files.dat.
In order to conduct the WHAM analysis use the following terminal command:
gmx_d wham -it tpr-files.dat -if pullf-files.
dat -o profile.xvg –hist histo.xvg -unit
kCal -bs-method b-his -nBootstrap 100 -bsres
The –it and –if options provide the WHAM module with the tpr
and force files, respectively. The output option (−o) provides the output file profile.xvg which contains the PMF plot for the process under
study, while the –hist provides the histo.xvg file which contains the
histograms of the process. The histogram analysis ensures that the
sampling around a reaction coordinate is adequate. An indication of
adequate sampling is a good overlap between the histograms of each
consequent window, as illustrated in Fig. 13. The –unit option defines
the unit for the energy value (in this case, the chemically relevant unit
of kcal/mol is preferred). The –bs method option is used in order to
define the error analysis method. In this case, we provide the keyword b-his in order to use the Bayesian bootstrap method for our
error analysis. With this method, complete histograms are considered
as independent data points, and the bootstrap is carried out by assigning random weights to the histograms. The –nBootstrap provides the
number of bootstraps to be used for the error analysis, in this case
100. For further details on the statistical analysis, please refer to reference [7]. The –bsres option provides the output of the Bootstrap
analysis which is a .xvg file containing the PMF plot along with the
standard deviations in energy.
Following these steps, the umbrella sampling simulation will
be completed. The results for CC:2-HP-B-CD complex are presented and briefly discussed in Fig. 14.
3.6.2 Run the WHAM
Analysis
Sofia Kiriakidi and Thomas Mavromoustakos