[gmx-users] Error while running free energy simulation.
Mark Abraham
mark.j.abraham at gmail.com
Wed Nov 19 16:22:10 CET 2014
On Wed, Nov 19, 2014 at 2:50 PM, vivek sharma <viveksharma.iitb at gmail.com>
wrote:
> 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.
>
Only if you can show that your observables are tolerant of the known
weaknesses in the ensemble produced by Berensden coupling.
> 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?
>
Observing stable values of a range of observables is the usual way. In your
case, I would recommend including the total pressure, also. Equilibrate
first with Berendsen to get close to the stable regime, then switch to PR.
Mark
> 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
> >
> > ==================================================
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at http://www.gromacs.org/
> > Support/Mailing_Lists/GMX-Users_List before posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>
More information about the gromacs.org_gmx-users
mailing list