Hi Sagar, At which time step do you get LINCS warnings?
Also, please see: http://www.gromacs.org/Documentation/Errors#LINCS.2fSETTLE.2fSHAKE_warnings Dan On Tue, Aug 28, 2018 at 3:19 AM sagar bathla <sagarbath...@gmail.com> wrote: > Dear all, > > My system consists of 2 orthorhombic parallel graphene sheets in a big > triclinic box filled with water. when i am trying to run equillibration > then i am getting too many lincs warnings and simulation has been getting > crashed everytime. i have put retraint on all atoms of graphene but still > this problem is occuring again. > > My .mdp file looks like this > title = OPLS Graphene IN WATER NVT equilibration > define = -DPOSRES -DFLEXIBLE ; position restrain the protein > > ; Run parameters > integrator = md ; leap-frog integrator > nsteps = 500000 ; 2 * 500000 = 1000 ps > > dt = 0.002 ; 2 fs > > ; Output control > nstxout = 1000 ; save coordinates every 1.0 ps > nstvout = 1000 ; save velocities every 1.0 ps > nstenergy = 1000 ; save energies every 1.0 ps > nstlog = 1000 ; update log file every 1.0 ps > > ; Bond parameters > continuation = yes ; 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 > lincs-warnangle = 90 > > ; Neighborsearching > vdw-modifier = Force-switch > cutoff-scheme = Verlet > ns_type = grid ; search neighboring grid cells > nstlist = 10 ; 20 fs, largely irrelevant with > Verlet > rcoulomb = 1.2 ; short-range electrostatic cutoff > (in nm) > rvdw = 1.2 > rlist = 1.2 ; short-range van der Waals cutoff > (in nm) > rvdw-switch = 1.0 > ; Electrostatics > coulombtype = PME ; Particle Mesh Ewald for long-range > electrostatics > pme_order = 4 ; cubic interpolation > fourierspacing = 0.16 ; grid spacing for FFT > > ; Temperature coupling is on > tcoupl = nose-hoover ; nose-hoover thermostat > tc-grps = GRA SOL ; 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 is off > pcoupl = no ; no pressure coupling in NVT > > ; Periodic boundary conditions > pbc = xyz ; 3-D PBC > periodic-molecules = yes > > ; Dispersion correction > DispCorr = EnerPres ; account for cut-off vdW scheme > > ; number of steps for center of mass motion removal = > comm-mode = Linear > nstcomm = 1 > comm-grps = GRA SOL > ; Velocity generation > gen_vel = no ; assign velocities from Maxwell > distribution > gen_temp = 300 ; temperature for Maxwell distribution > gen_seed = -1 ; generate a random seed > > ;non equillibrium md > freezegrps: GRA > freezedim: Y Y Y > i have tried various things but nothing is working. > please help to solve this problem > > Regards > Sagar Bathla > -- > 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? 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.