[gmx-users] salvation free energy - gmx bar

[Javier Luque Di Salvo]

Hello Shadfar,

Check your mdp files for missing/repeated init-lambda-state. I had the same
problem, in my case I had two xvg file corresponding to the same
init-lambda-state and in consequence one of them was missing

Cheers
Javier

Date: Thu, 11 Jan 2018 23:33:28 +0000
> From: "Shadfar, Shamim" <Z.Shadfar at massey.ac.nz>
> To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
> Subject: [gmx-users] salvation free energy - gmx bar
> Message-ID:
>         <
> MEXPR01MB02309BF58F609357A035F9DBC3160 at MEXPR01MB0230.ausprd01.prod.outlook.com
> >
>
> Content-Type: text/plain; charset="iso-8859-1"
>
> 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
>
> lambdas:
>
> 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
>
> <http://www.gromacs.org/Documentation/Errors>
>
>
>
>
> ------------------------------
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>
> End of gromacs.org_gmx-users Digest, Vol 165, Issue 41
> ******************************************************
>