It sounds like you are only running one free energy simulation. You need to
run one simulation for each lambda (changing "init-lambda-state" in your
mdp file) and name the dhdl xvg file a different name for each one.
On Mon, Mar 19, 2018 at 8:30 AM, Javier Luque Di Salvo <
jluquedisa...@gmail.com> wrote:
> 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*
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--
James "Wes" Barnett
Postdoctoral Research Scientist
Department of Chemical Engineering
Kumar Research Group <http://www.columbia.edu/cu/kumargroup/>
Columbia University
w.barn...@columbia.edu
http://wbarnett.us
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