Hi Agnivo, What is the rationale for ignoring the long bond warning?
Cheers, Tsjerk On May 5, 2015 17:41, "Agnivo Gosai" <agnivogromac...@gmail.com> wrote: > Dear Users, > > I have a solvated protein-dna structure placed inside a simulation box. > During topology preparation and subsequent steps I did not receive any > warning , except a long bond warning in the pdb2gmx step for the protein. > > I then did an energy minimization. The script is shown below: > > ; For energy minimization > ; Parameters describing what to do, when to stop and what to save > integrator = steep ; Algorithm (steep = steepest descent minimization) > emtol = 500.0 ; Stop minimization when the maximum force < 1000.0 > kJ/mol/nm > emstep = 0.01 ; Energy step size > nsteps = 500000 ; Maximum number of (minimization) steps to > perform > energygrps = System ; Which energy group(s) to write to disk > > > ; Parameters describing how to find the neighbors of each atom and how to > calculate the interactions > nstlist = 1 ; Frequency to update the neighbor list and long > range forces > ns_type = grid ; Method to determine neighbor list (simple, grid) > rlist = 1.4 ; Cut-off for making neighbor list (short range > forces) > coulombtype = PME ; Treatment of long range electrostatic > interactions > rcoulomb = 1.4 ; Short-range electrostatic cut-off > rvdw = 1.4 ; Short-range Van der Waals cut-off > pbc = xyz ; Periodic Boundary Conditions > > This is the result at the end of the minimization : > > Steepest Descents converged to Fmax < 500 in 8938 steps > Potential Energy = -7.5707590e+06 > Maximum force = 4.4626624e+02 on atom 2581 > Norm of force = 3.2807171e+00 > > Then I proceeded for a 5 ns NVT equilibration , with the following script : > > title = NVT equilibration > define = -DPOSRES ; position restrain the protein and ligand > ; Run parameters > integrator = md ; leap-frog integrator > nsteps = 2500000 ; 5 ns > dt = 0.002 ; 2 fs > ; Output control > nstxout = 500 ; save coordinates every 1 ps > nstvout = 500 ; save velocities every 1 ps > nstenergy = 500 ; save energies every 1 ps > nstlog = 500 ; update log file every 1 ps > nstxtcout = 1000 ; > ; Bond parameters > continuation = no ; first dynamics run > constraint_algorithm = lincs ; holonomic constraints > constraints = all-bonds ; all bonds (even heavy atom-H bonds) > constrained > lincs_iter = 1 ; accuracy of LINCS > lincs_order = 4 ; also related to accuracy > ; Neighborsearching > ns_type = grid ; search neighboring grid cells > nstlist = 5 ; 10 fs > rlist = 1.4 ; short-range neighborlist cutoff (in nm) > rcoulomb = 1.4 ; short-range electrostatic cutoff (in nm) > rvdw = 1.4 ; short-range van der Waals cutoff (in nm) > ; Electrostatics > coulombtype = PME ; Particle Mesh Ewald for long-range > electrostatics > pme_order = 4 ; cubic interpolation > fourierspacing = 0.16 ; grid spacing for FFT > ; Temperature coupling > tcoupl = V-rescale ; modified Berendsen thermostat > tc-grps = DNA_Protein Water_and_ions ; two coupling groups - more > accurate > tau_t = 0.1 0.1 ; time constant, in ps > ref_t = 300 300 ; reference temperature, one > for each group, in K > ; Pressure coupling > pcoupl = no ; no pressure coupling in NVT > ; Periodic boundary conditions > pbc = xyz ; 3-D PBC > ; Dispersion correction > DispCorr = EnerPres ; account for cut-off vdW scheme > ; Velocity generation > gen_vel = yes ; assign velocities from Maxwell distribution > gen_temp = 300 ; temperature for Maxwell distribution > gen_seed = -1 ; generate a random seed > ; COM motion removal > ; These options remove COM motion of the system > nstcomm = 10 > comm-mode = Linear > comm-grps = System > > However the simulation crashed and the following error messages were > received : > > step 103336: Water molecule starting at atom 369120 can not be settled. > Check for bad contacts and/or reduce the timestep if appropriate. > > step 103336: Water molecule starting at atom 356715 can not be settled. > Check for bad contacts and/or reduce the timestep if appropriate. > > ------------------------------------------------------- > Program mdrun_mpi, VERSION 4.6.7 > Source code file: > /work/gb_lab/agosai/GROMACS/gromacs-4.6.7/src/mdlib/pme.c, line: 851 > > Fatal error: > 1 particles communicated to PME node 11 are more than 2/3 times the cut-off > out of the domain decomposition cell of their charge group in dimension y. > This usually means that your system is not well equilibrated. > > > Now, what can be going wrong in here ? Do I need to do more energy > minimization , using other algorithms? Or , should I be heating up my > system gradually to 300 K ( from 270 K , for e.g.) and then do a NVT > equilibration at 300 K? > > Kindly suggest. > > > Thanks & Regards > Agnivo Gosai > Grad Student, Iowa State University. > -- > 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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