Sorry, if the attachments don't load, here are the uploaded texts. Thank you once again,
Angelina *Job submission: * #!/bin/bash # Set some environment variables FREE_ENERGY=`pwd` echo "Free energy home directory set to $FREE_ENERGY" MDP=$FREE_ENERGY/MDP echo ".mdp files are stored in $MDP" # Change to the location of your GROMACS-2018 installation GMX=/usr/local/gromacs/bin for (( i=0; i<22; i++ )) do LAMBDA=$i # A new directory will be created for each value of lambda and # at each step in the workflow for maximum organization. mkdir Lambda_$LAMBDA cd Lambda_$LAMBDA ############################## # ENERGY MINIMIZATION STEEP # ############################## echo "Starting minimization for lambda = $LAMBDA..." mkdir EM cd EM # Iterative calls to grompp and mdrun to run the simulations $GMX/gmx grompp -f $MDP/EM/em_steep_$LAMBDA.mdp -c $FREE_ENERGY/curcumin/solv_curenol_54a7.gro -p $FREE_ENERGY/curcumin/topol.top -o min$LAMBDA.tpr $GMX/gmx mdrun -deffnm min$LAMBDA -ntmpi 1 sleep 10 ##################### # NVT EQUILIBRATION # ##################### echo "Starting constant volume equilibration..." cd ../ mkdir NVT cd NVT $GMX/gmx grompp -f $MDP/NVT/nvt_$LAMBDA.mdp -c ../EM/min$LAMBDA.gro -p $FREE_ENERGY/curcumin/topol.top -o nvt$LAMBDA.tpr $GMX/gmx mdrun -deffnm nvt$LAMBDA -ntmpi 1 echo "Constant volume equilibration complete." sleep 10 ##################### # NPT EQUILIBRATION # ##################### echo "Starting constant pressure equilibration..." cd ../ mkdir NPT cd NPT $GMX/gmx grompp -f $MDP/NPT/npt_$LAMBDA.mdp -c ../NVT/nvt$LAMBDA.gro -p $FREE_ENERGY/curcumin/topol.top -t ../NVT/nvt$LAMBDA.cpt -o npt$LAMBDA.tpr $GMX/gmx mdrun -deffnm npt$LAMBDA -ntmpi 1 echo "Constant pressure equilibration complete." sleep 10 ################# # PRODUCTION MD # ################# echo "Starting production MD simulation..." cd ../ mkdir Production_MD cd Production_MD $GMX/gmx grompp -f $MDP/Production_MD/md_$LAMBDA.mdp -c ../NPT/npt$LAMBDA.gro -p $FREE_ENERGY/curcumin/topol.top -t ../NPT/npt$LAMBDA.cpt -o md$LAMBDA.tpr $GMX/gmx mdrun -deffnm md$LAMBDA -ntmpi 1 echo "Production MD complete." # End echo "Ending. Job completed for lambda = $LAMBDA" cd $FREE_ENERGY done exit; *MDP input file:* ; Run control integrator = steep nsteps = 5000 ; EM criteria and other stuff emtol = 100 emstep = 0.01 niter = 20 nbfgscorr = 10 ; Output control nstlog = 1 nstenergy = 1 ; Neighborsearching and short-range nonbonded interactions cutoff-scheme = verlet nstlist = 1 ns_type = grid pbc = xyz rlist = 1.2 ; Electrostatics coulombtype = PME rcoulomb = 1.2 ; van der Waals vdwtype = cutoff vdw-modifier = potential-switch rvdw-switch = 1.0 rvdw = 1.2 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = EnerPres ; Spacing for the PME/PPPM FFT grid fourierspacing = 0.12 ; EWALD/PME/PPPM parameters pme_order = 6 ewald_rtol = 1e-06 epsilon_surface = 0 ; Temperature and pressure coupling are off during EM tcoupl = no pcoupl = no ; Free energy control stuff free_energy = yes init_lambda_state = 21 delta_lambda = 0 calc_lambda_neighbors = 1 ; only immediate neighboring windows couple-moltype = CUR ; name of moleculetype to decouple couple-lambda0 = vdw ; only van der Waals interactions couple-lambda1 = none ; turn off everything, in this case only vdW couple-intramol = no ; Vectors of lambda specified here ; Each combination is an index that is retrieved from init_lambda_state for each simulation ; init_lambda_state 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 vdw_lambdas = 0.00 0.005 0.01 0.025 0.05 0.075 0.10 0.20 0.30 0.40 0.50 0.60 0.65 0.70 0.75 0.80 0.85 0.90 0.90 0.95 1.00 coul_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 ; We are not transforming any bonded or restrained interactions bonded_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 restraint_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 ; Masses are not changing (particle identities are the same at lambda = 0 and lambda = 1) mass_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 ; Not doing simulated temperting here temperature_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 ; Options for the decoupling sc-alpha = 0.5 sc-coul = no ; linear interpolation of Coulomb (none in this case) sc-power = 1 sc-sigma = 0.3 nstdhdl = 10 ; No velocities during EM gen_vel = no ; options for bonds constraints = h-bonds ; we only have C-H bonds here ; Type of constraint algorithm constraint-algorithm = lincs ; Do not constrain the starting configuration continuation = no ; Highest order in the expansion of the constraint coupling matrix lincs-order = 12 On Fri, Feb 8, 2019 at 2:50 PM Angelina Malagodi <angelinamalag...@gmail.com> wrote: > I am trying to calculate the free energy of curcumin in water. My system > goes from 0- 21 lambdas, but it is not recognizing my final lambda. I am > sure that I have 21 transitions for vdw_lambdas, coul_lambdas, > bounded_lambdas, resistant_lambdas, mass_lambdas, and temperature_lambdas. > I do not understand why the 21st lambda is not being recognized. My job > script, input file, and error are attached. Thank you so much for your > time and help! > > Sincerely, > Angelina Malagodi > > > ERROR 1 [file > /Users/tyemartin/Documents/Free_Energy/MDP/EM/em_steep_21.mdp]: > > initial thermodynamic state 21 does not exist, only goes to 20 > > > -- 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.