[gmx-users] Fatal Lambda error

Angelina Malagodi angelinamalagodi at gmail.com
Mon Feb 11 21:05:34 CET 2019


Hello,

I'm sorry I don't think I understood fully, so just as a clarification. Is
it possible to go from 0 through 21? If so, which line of the mdp file do I
change so that it will recognize the full range?

Thank you so much,

Angelina Malagodi

On Sun, Feb 10, 2019 at 3:03 AM Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> As Magnus hinted, the valid range for i is 0 to 20, so change the bash
> script so that it does not reach 21.
>
> Mark
>
> On Sat., 9 Feb. 2019, 10:26 Magnus Lundborg, <
> magnus.lundborg at scilifelab.se>
> wrote:
>
> > 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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