[gmx-users] Fatal Lambda error
Justin Lemkul
jalemkul at vt.edu
Mon Feb 11 21:11:09 CET 2019
On 2/11/19 3:05 PM, Angelina Malagodi wrote:
> 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?
There are 21 states. The first state is 0. Therefore, your valid state
indices are 0..20. You cannot access lambda state 21, because in a
zero-based index scheme, that would actually be the 22nd state.
As stated before, your bash script should use for (( i=0; i<21; i++ ))
-Justin
> 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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--
==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall
Virginia Tech Department of Biochemistry
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