[gmx-users] Error while running free energy simulation.
vivek sharma
viveksharma.iitb at gmail.com
Wed Nov 19 14:50:24 CET 2014
Dear Justin,
Thanks for ypour reply.
My runs are getting failed at multiple lambda values, say 4 out of 21. For
some cases, these runs go fine when I change pcouple to berendsen. Is it
acceptable to use berendsen instead of PR for such simulations.
I guess I need to do more equilibration on my system as my runs are getting
failed at production run phase. How will I decide the end point for
equilibration?
Thanks and regards,
Vivek
On 11 November 2014 18:03, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> 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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