[gmx-users] Fatal Lambda error
Angelina Malagodi
angelinamalagodi at gmail.com
Fri Feb 8 23:08:04 CET 2019
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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