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 <jalem...@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 > > jalem...@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-requ...@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? 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