[gmx-users] Fatal Lambda error

Magnus Lundborg magnus.lundborg at scilifelab.se
Sat Feb 9 10:25:45 CET 2019


The lambda states are numbered from 0. You only have 21 different states in
your mdp file. Therefore your init-lambda-state can range from 0 to 20.

Cheers,

Magnus

Den fre 8 feb. 2019 23:08 skrev Angelina Malagodi <
angelinamalagodi at gmail.com>:

> 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 <
> angelinamalagodi at 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
> >
> >
> >
> --
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