[gmx-users] salvation free energy - gmx bar

Shadfar, Shamim Z.Shadfar at massey.ac.nz
Fri Jan 12 00:33:42 CET 2018

Hello everyone,

I am doing solvation free energy calculation for a small system (Thermodynamic Integration). At the analysis step, gmx bar (gmx bar -f md*.xvg -o -oi -oh), I am facing this error, which I never had before. I have all my md.xvg files.

Could anyone help me with that?

Here is the error:

md9.xvg: Ignoring set 'pV (kJ/mol)'.

md9.xvg: 0.0 - 10000.0; lambda = (0, 0.9, 0, 0, 0)

    dH/dl & foreign lambdas:

        dH/dl (mass-lambda) (500001 pts)

        dH/dl (coul-lambda) (500001 pts)

        dH/dl (vdw-lambda) (500001 pts)

        dH/dl (bonded-lambda) (500001 pts)

        dH/dl (restraint-lambda) (500001 pts)

        delta H to (0, 0.8, 0, 0, 0) (500001 pts)

        delta H to (0, 0.9, 0, 0, 0) (500001 pts)

        delta H to (0, 1, 0, 0, 0) (500001 pts)

Writing histogram to histogram.xvg

Back Off! I just backed up histogram.xvg to ./#histogram.xvg.1#


Program:     gmx bar, version 2016.3

Source file: src/gromacs/gmxana/gmx_bar.cpp (line 1174)

Fatal error:

There is no path between the states X & Y below that is covered by foreign


cannot proceed with BAR.

Use thermodynamic integration of dH/dl by calculating the averages of dH/dl

with g_analyze and integrating them.

Alternatively, use the -extp option if (and only if) the Hamiltonian

depends linearly on lambda, which is NOT normally the case.

lambda vector [X]:  init-lambda-state=5 (mass-lambda) l=0 (coul-lambda) l=0.5

(vdw-lambda) l=0 (bonded-lambda) l=0 (restraint-lambda) l=0

lambda vector [Y]:  init-lambda-state=7 (mass-lambda) l=0 (coul-lambda) l=0.7

(vdw-lambda) l=0 (bonded-lambda) l=0 (restraint-lambda) l=0

For more information and tips for troubleshooting, please check the GROMACS

website at http://www.gromacs.org/Documentation/Errors

Shamim Shadfar

PhD Candidate at Massey University
Institute of Natural and Mathematical Sciences (INMS)
Centre of Theoretical Chemistry and Physics (CTCP)

Auckland, New Zealand


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