[gmx-users] Free Energy solvation generate multiple dhdl.xvg output files

[Javier Luque Di Salvo]

Dear Gromacs users,
I am trying to run Free Energy calculations of a single ion in water (to
calculate its solvation energy). Since this is a new topic for me, I am
following the tutorial 'Solvation free energy of ethanol' (easily find in
google). The three steps work well without erros (1-energy minimization,
2-equilibration, 3-lambda (de)coupling) but I am not obtaining the separate
dhdl.xvg files after the step 3, only a single output file run.xvg. The
reason for this is that in the tutorial, a script named mklambdas.sh is
used to generate such separate files in separate folders. Since I would
like to keep track of the .mdp strings and understand how they work, I am
not using this script, instead I am trying to properly define mdp commands:

_________________________________________
; Free energy variables
free-energy              = yes
couple-moltype           = NH4
couple-lambda0           = none
couple-lambda1           = vdwq
couple-intramol          = no
init-lambda              = -1
init-lambda-state        = 0
delta-lambda             = 0
nstdhdl                  = 50
fep-lambdas              = 0.0 0.2 0.4 0.6 0.8 0.9 1.0
mass-lambdas             =
coul-lambdas             =
vdw-lambdas              =
bonded-lambdas           =
restraint-lambdas        =
temperature-lambdas      =
calc-lambda-neighbors    = 1
init-lambda-weights      =
dhdl-print-energy        = no
sc-alpha                 = 1.0
sc-power                 = 1
sc-r-power               = 6
sc-sigma                 = 0.3
sc-coul                  = no
separate-dhdl-file       = yes
dhdl-derivatives         = yes
dh_hist_size             = 0
dh_hist_spacing          = 0.1
_________________________________________

When trying to use "gmx bar -f run.xvg -g run.edr -o bar.xvg" I get this
error:
_______________________________________________________
run.xvg: Ignoring set 'pV (kJ/mol)'.
run.xvg: 0.0 - 200.0; lambda = 0
    dH/dl & foreign lambdas:
        dH/dl (fep-lambda) (2001 pts)
        delta H to 0 (2001 pts)
        delta H to 0.2 (2001 pts)

Opened run.edr as single precision energy file
Reading energy frame      0 time    0.000
-------------------------------------------------------
Program:     gmx bar, version 2016.4
Source file: src/gromacs/gmxana/gmx_bar.cpp (line 3286)
Fatal error:
Did not find delta H information in file run.edr
____________________________________________________

This is the run.xvg output file:

____________________________________________________
# Command line:
#   gmx mdrun -ntmpi 2 -ntomp 8 -pin on -v -deffnm run
# gmx mdrun is part of G R O M A C S:
#
# S  C  A  M  O  R  G
#
@    title "dH/d\xl\f{} and \xD\f{}H"
@    xaxis  label "Time (ps)"
@    yaxis  label "dH/d\xl\f{} and \xD\f{}H (kJ/mol [\xl\f{}]\S-1\N)"
@TYPE xy
@ subtitle "T = 300 (K) \xl\f{} state 0: fep-lambda = 0.0000"
@ view 0.15, 0.15, 0.75, 0.85
@ legend on
@ legend box on
@ legend loctype view
@ legend 0.78, 0.8
@ legend length 2
@ s0 legend "dH/d\xl\f{} fep-lambda = 0.0000"
@ s1 legend "\xD\f{}H \xl\f{} to 0.0000"
@ s2 legend "\xD\f{}H \xl\f{} to 0.2000"
@ s3 legend "pV (kJ/mol)"
0.0000 -530.14746 0.0000000 -106.84067 9.7838984
0.1000 -177.17302 0.0000000 -33.945797 9.7844772
0.2000 -158.46501 0.0000000 -30.541293 9.7854595
0.3000 -143.72632 0.0000000 -27.669909 9.7857714
(...)

____________________________________________________


Could you guide me through a proper string definition in the mdp options to
get separate files, in order to use the BAR algorithm afterwards?

Best regards

*Javier*