[gmx-users] Error while running free energy simulation.
Justin Lemkul
jalemkul at vt.edu
Tue Nov 11 13:33:47 CET 2014
On 11/11/14 2:12 AM, vivek sharma wrote:
> Dear Users,
> I am trying to replicate the free energy tutorial by Dr Justin. In my
> attempt I have calculated the OPLS-AA FF parameters for my molecules of
> interest using acpype. I made the system in water and 1-octanol, While
> running the independent lambda simulation for both the systems, I got an
> error while running the simulation for 1-octanol system whereas the
> simulation for water system were successful.
>
> Following is the error message reported in failed simulation for 1-octanol
> system
Which lambda state fails? Or is it multiple? Does failure occur during
equilibration or production? If the latter, you probably just need to
equilibrate more thoroughly. If the former, energy-minimize more rigorously.
-Justin
> ------------------------------------------------------------------
> WARNING: Listed nonbonded interaction between particles 842 and 851
> at distance 427.422 which is larger than the table limit 2.200 nm.
>
> This is likely either a 1,4 interaction, or a listed interaction inside
> a smaller molecule you are decoupling during a free energy calculation.
> Since interactions at distances beyond the table cannot be computed,
> they are skipped until they are inside the table limit again. You will
> only see this message once, even if it occurs for several interactions.
>
> IMPORTANT: This should not happen in a stable simulation, so there is
> probably something wrong with your system. Only change the table-extension
> distance in the mdp file if you are really sure that is the reason.
>
> -----------------------------------------------------------------
>
> I tried running the same system without free energy option ( free_energy
> = no), which was successful. It has narrowed the reason for
> error to be the free energy code.
> It will be really helpful if anybody can help me in understanding the
> probable reason for error and any directions for handling this error.
>
> Pasting below the mdp options for one of the independent lambda simulation
> for reference.
> -----------------------------------------------------------------------------------------------------------
> ; Run control
> integrator = sd ; Langevin dynamics
> tinit = 0
> dt = 0.002
> nsteps = 2500000 ; 5 ns
> nstcomm = 100
> ; Output control
> nstxout = 500
> nstvout = 500
> nstfout = 0
> nstlog = 500
> nstenergy = 500
> nstxout-compressed = 0
> ; Neighborsearching and short-range nonbonded interactions
> cutoff-scheme = verlet
> nstlist = 20
> 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 coupling
> ; tcoupl is implicitly handled by the sd integrator
> tc_grps = system
> tau_t = 1.0
> ref_t = 300
> ; Pressure coupling is on for NPT
> Pcoupl = Parrinello-Rahman
> tau_p = 1.0
> compressibility = 4.5e-05
> ref_p = 1.0
> ; Free energy control stuff
> free_energy = yes
> init_lambda_state = 0
> delta_lambda = 0
> calc_lambda_neighbors = 1 ; only immediate neighboring windows
> ; 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
> vdw_lambdas = 0.00 0.10 0.20 0.30 0.40 0.50 0.60 0.70 0.80
> 0.90 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 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 0.10 0.20 0.30 0.40 0.50 0.60 0.70 0.80 0.90 1.00
> ; 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 = 1.0
> sc-sigma = 0.3
> couple-moltype = FEL ; name of moleculetype to decouple
> couple-lambda0 = none ; only van der Waals interactions
> couple-lambda1 = vdw-q ; turn off everything, in this case
> only vdW
> couple-intramol = no
> nstdhdl = 10
> ; Do not generate velocities
> gen_vel = no
> ; options for bonds
> constraints = all-bonds ; we only have C-H bonds here
> ; Type of constraint algorithm
> constraint-algorithm = lincs
> ; Constrain the starting configuration
> ; since we are continuing from NPT
> continuation = yes
> ; Highest order in the expansion of the constraint coupling matrix
> lincs-order = 12
> ------------------------------------------------------------------------------------------------------------
>
> Thanks in advance
>
> regards,
> Vivek Sharma
>
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
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