Try using -DFLEXIBLE in your minimization prior to running NVT. MZ
On Tue, Jul 9, 2013 at 10:22 AM, ashish24294 <ashish24...@yahoo.co.in>wrote: > I am simulating one urea molecule in water and am struggling with it > nvt.log > <http://gromacs.5086.x6.nabble.com/file/n5009701/nvt.log> > > > > *The .mdp for energy minimization is* > > ; minim.mdp - used as input into grompp to generate em.tpr > ; Parameters describing what to do, when to stop and what to save > integrator = steep ; Algorithm (steep = steepest descent > minimization) > emtol = 100.0 ; Stop minimization when the maximum force > < 1000.0 > kJ/mol/nm > emstep = 0.01 ; Energy step size > nsteps = 50000 ; Maximum number of (minimization) steps > to perform > energygrps = URE > > ; 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 = 1.0 ; Cut-off for making neighbor list (short > range forces) > coulombtype = PME ; Treatment of long range electrostatic > interactions > rcoulomb = 1.0 ; Short-range electrostatic cut-off > rvdw = 1.0 ; Short-range Van der Waals cut-off > pbc = xyz ; Periodic Boundary Conditions (yes/no) > > > > > /*And the nvt.mdp is: > */ > title = UREA_in_WATER NVT equillibration > > ; Run parameters > integrator = md ; leap-frog integrator > nsteps = 50000 ; 2 * 50000 = 100 ps > dt = 0.002 ; 2 fs > ; Output control > nstxout = 100 ; save coordinates every 0.2 ps > nstvout = 100 ; save velocities every 0.2 ps > nstenergy = 100 ; save energies every 0.2 ps > nstlog = 100 ; update log file every 0.2 ps > energygrps = URE > ; 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 = 0.75 ; short-range neighborlist cutoff (in nm) > rcoulomb = 0.75 ; short-range electrostatic cutoff (in nm) > rvdw = 0.75 ; 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 = URE_Water ; two coupling groups - more accurate > tau_t = 0.1 ; time constant, in > ps > ref_t = 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 > > *The resultant nvt.log has been attached* > > > > -- > View this message in context: > http://gromacs.5086.x6.nabble.com/Multiple-LINCS-Warnings-in-NVT-Equillibration-tp5009701.html > Sent from the GROMACS Users Forum mailing list archive at Nabble.com. > -- > gmx-users mailing list gmx-users@gromacs.org > 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 gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists