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* -- 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-requ...@gromacs.org.