[gmx-users] Fatal Lambda error
Mark Abraham
mark.j.abraham at gmail.com
Sun Feb 10 11:02:35 CET 2019
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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