On Wed, Nov 19, 2014 at 2:50 PM, vivek sharma <viveksharma.i...@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 <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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