Hi all! I have been running a series of simulations for coupling a molecule (free energy calculations). All my settings and parameters in the mdp file worked great for one system, but then I change the molecule to a bigger one and I started to have warnings about 1-4 interactions:
Warning: 1-4 interaction between 1 and 143 at distance 2.579 which is larger than the 1-4 table size 2.500 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file or with user tables increase the table size I made severals tests to find the error: minimization, nvt, mdp and md without the Free Energy settings and It ran without the warning. So I guess the warning must be related to the FE implementation. However, I'm clueless about what can I change to stop having that warning. I already read other posts but I'm still the same. Should I just ignore it? Also, the initial structure is the result of a md simulation, so I don't know what can be wrong in the topology or mdp file. Should I change the continuation parameter (continuation=yes) for the minimization and the nvt? Energy minimization converged but not to machine precision: Converged to machine precision, but not to the requested precision Fmax < 100 Double precision normally gives you higher accuracy. You might need to increase your constraint accuracy, or turn off constraints alltogether (set constraints = none in mdp file) writing lowest energy coordinates. Steepest Descents converged to machine precision in 481 steps, but did not reach the requested Fmax < 100. Potential Energy = -7.8070088e+05 Maximum force = 7.6036969e+02 on atom 68 Norm of force = 2.3164215e+01 This is the copy of the mdp file (based os Justin Lemluk's tutorial), I'm using GROMACS 4.5.4. title = steepest descent energy minimization ; Run control integrator = steep nsteps = 30000 ; EM criteria and other stuff emtol = 100 emstep = 0.01 niter = 20 nbfgscorr = 10 ; Output control nstlog = 1 nstenergy = 1 ; Neighborsearching and short-range nonbonded interactions nstlist = 1 ns_type = grid pbc = xyz periodic-molecules = yes rlist = 1.5 ; Electrostatics coulombtype = PME rcoulomb = 1.5 ; van der Waals vdw-type = switch rvdw-switch = 0.8 rvdw = 0.9 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = EnerPres ; Spacing for the PMEPPPM FFT grid fourierspacing = 0.12 ; EWALDPMEPPPM parameters pme_order = 6 ewald_rtol = 1e-06 epsilon_surface = 0 optimize_fft = no ; Temperature and pressure coupling are off during EM tcoupl = no pcoupl = no ; Free energy control stuff free_energy = yes init_lambda = 1.0 delta_lambda = 0 foreign_lambda = 0.95 sc-alpha = 0 sc-power = 0 sc-sigma = 0 couple-moltype = Protein_chain_A ; name of moleculetype to decouple couple-lambda0 = vdw ; only vdw interactions couple-lambda1 = vdw-q ; all interactions couple-intramol = no nstdhdl = 10 ; Generate velocities to start gen_vel = no ; options for bonds constraints = none ; we only have C-H bonds here ; Type of constraint algorithm constraint-algorithm = lincs ; Do not constrain the starting configuration continuation = no ; Highest order in the expansion of the constraint coupling matrix lincs-order = 12 Thank you in advance!! Sonia Aguilera Graduate assistant Chemical Engineering Department Universidad de los Andes -- View this message in context: http://gromacs.5086.x6.nabble.com/1-4-interactions-free-energy-calculations-tp5009364.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
