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**PROGRAM:**

**NAME**

gmx-bar - Calculate free energy difference estimates through Bennett's acceptance ratio

**SYNOPSIS**

gmx bar [

**-f**

__[<.xvg>__

__[...]]__] [

**-g**

__[<.edr>__

__[...]]__] [

**-o**

__[<.xvg>]__]

[

**-oi**

__[<.xvg>]__] [

**-oh**

__[<.xvg>]__] [

**-[no]w**] [

**-xvg**

__<enum>__]

[

**-b**

__<real>__] [

**-e**

__<real>__] [

**-temp**

__<real>__] [

**-prec**

__<int>__]

[

**-nbmin**

__<int>__] [

**-nbmax**

__<int>__] [

**-nbin**

__<int>__] [

**-[no]extp**]

**DESCRIPTION**

**gmx**

**bar**calculates free energy difference estimates through Bennett's acceptance ratio

method (BAR). It also automatically adds series of individual free energies obtained with

BAR into a combined free energy estimate.

Every individual BAR free energy difference relies on two simulations at different states:

say state A and state B, as controlled by a parameter, lambda (see the

__.mdp__parameter

**init_lambda**). The BAR method calculates a ratio of weighted average of the Hamiltonian

difference of state B given state A and vice versa. The energy differences to the other

state must be calculated explicitly during the simulation. This can be done with the

__.mdp__

option

**foreign_lambda**.

Input option

**-f**expects multiple

**dhdl.xvg**files. Two types of input files are supported:

· Files with more than one

__y__-value. The files should have columns with dH/dlambda and

Deltalambda. The lambda values are inferred from the legends: lambda of the

simulation from the legend of dH/dlambda and the foreign lambda values from the

legends of Delta H

· Files with only one

__y__-value. Using the

**-extp**option for these files, it is assumed

that the

__y__-value is dH/dlambda and that the Hamiltonian depends linearly on lambda.

The lambda value of the simulation is inferred from the subtitle (if present),

otherwise from a number in the subdirectory in the file name.

The lambda of the simulation is parsed from

**dhdl.xvg**file's legend containing the string

'dH', the foreign lambda values from the legend containing the capitalized letters 'D' and

'H'. The temperature is parsed from the legend line containing 'T ='.

The input option

**-g**expects multiple

__.edr__files. These can contain either lists of energy

differences (see the

__.mdp__option

**separate_dhdl_file**), or a series of histograms (see the

__.mdp__options

**dh_hist_size**and

**dh_hist_spacing**). The temperature and lambda values are

automatically deduced from the

**ener.edr**file.

In addition to the

__.mdp__option

**foreign_lambda**, the energy difference can also be

extrapolated from the dH/dlambda values. This is done with the``-extp`` option, which

assumes that the system's Hamiltonian depends linearly on lambda, which is not normally

the case.

The free energy estimates are determined using BAR with bisection, with the precision of

the output set with

**-prec**. An error estimate taking into account time correlations is

made by splitting the data into blocks and determining the free energy differences over

those blocks and assuming the blocks are independent. The final error estimate is

determined from the average variance over 5 blocks. A range of block numbers for error

estimation can be provided with the options

**-nbmin**and

**-nbmax**.

**gmx**

**bar**tries to aggregate samples with the same 'native' and 'foreign' lambda values, but

always assumes independent samples.

**Note**that when aggregating energy

differences/derivatives with different sampling intervals, this is almost certainly not

correct. Usually subsequent energies are correlated and different time intervals mean

different degrees of correlation between samples.

The results are split in two parts: the last part contains the final results in kJ/mol,

together with the error estimate for each part and the total. The first part contains

detailed free energy difference estimates and phase space overlap measures in units of kT

(together with their computed error estimate). The printed values are:

· lam_A: the lambda values for point A.

· lam_B: the lambda values for point B.

· DG: the free energy estimate.

· s_A: an estimate of the relative entropy of B in A.

· s_B: an estimate of the relative entropy of A in B.

· stdev: an estimate expected per-sample standard deviation.

The relative entropy of both states in each other's ensemble can be interpreted as a

measure of phase space overlap: the relative entropy s_A of the work samples of lambda_B

in the ensemble of lambda_A (and vice versa for s_B), is a measure of the 'distance'

between Boltzmann distributions of the two states, that goes to zero for identical

distributions. See Wu & Kofke, J. Chem. Phys. 123 084109 (2005) for more information.

The estimate of the expected per-sample standard deviation, as given in Bennett's original

BAR paper: Bennett, J. Comp. Phys. 22, p 245 (1976). Eq. 10 therein gives an estimate of

the quality of sampling (not directly of the actual statistical error, because it assumes

independent samples).

To get a visual estimate of the phase space overlap, use the

**-oh**option to write series of

histograms, together with the

**-nbin**option.

**OPTIONS**

Options to specify input files:

**-f**

**[<.xvg>**

**[...]]**

**(dhdl.xvg)**

**(Optional)**

xvgr/xmgr file

**-g**

**[<.edr>**

**[...]]**

**(ener.edr)**

**(Optional)**

Energy file

Options to specify output files:

**-o**

**[<.xvg>]**

**(bar.xvg)**

**(Optional)**

xvgr/xmgr file

**-oi**

**[<.xvg>]**

**(barint.xvg)**

**(Optional)**

xvgr/xmgr file

**-oh**

**[<.xvg>]**

**(histogram.xvg)**

**(Optional)**

xvgr/xmgr file

Other options:

**-[no]w**

**(no)**

View output

__.xvg__,

__.xpm__,

__.eps__and

__.pdb__files

**-xvg**

**<enum>**

xvg plot formatting: xmgrace, xmgr, none

**-b**

**<real>**

**(0)**

Begin time for BAR

**-e**

**<real>**

**(-1)**

End time for BAR

**-temp**

**<real>**

**(-1)**

Temperature (K)

**-prec**

**<int>**

**(2)**

The number of digits after the decimal point

**-nbmin**

**<int>**

**(5)**

Minimum number of blocks for error estimation

**-nbmax**

**<int>**

**(5)**

Maximum number of blocks for error estimation

**-nbin**

**<int>**

**(100)**

Number of bins for histogram output

**-[no]extp**

**(no)**

Whether to linearly extrapolate dH/dl values to use as energies

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