Hello gmx-users,<br><br>I have a 5 ang box with equal number of water and methanol molecules (1800), a neutral peptide, 8 hydroxide ions and 10 Li+ ions. The system is overall +2 charged.<br><br>I am trying to to do a NVT equilibration which runs into the following error:<br>
<br><br>t = 0.000 ps: Water molecule starting at atom 11816 can not be settled.<br>Check for bad contacts and/or reduce the timestep.<br><br>the nvt.mdp is:<br><br>title = hist NVT equilibration<br>define = -DPOSRES ; position restrain the protein<br>
; Run parameters<br>integrator = md ; leap-frog integrator<br>nsteps = 50000 ; 2 * 50000 = 100 ps<br>dt = 0.002 ; 2 fs<br>; Output control<br>nstxout = 100 ; save coordinates every 0.2 ps<br>nstvout = 100 ; save velocities every 0.2 ps<br>
nstenergy = 100 ; save energies every 0.2 ps<br>nstlog = 100 ; update log file every 0.2 ps<br>; Bond parameters<br>continuation = no ; first dynamics run<br>constraint_algorithm = lincs ; holonomic constraints<br>
constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained<br>lincs_iter = 1 ; accuracy of LINCS<br>lincs_order = 4 ; also related to accuracy<br>; Neighborsearching<br>ns_type = grid ; search neighboring grid cells<br>
nstlist = 5 ; 10 fs<br>rlist = 1.0 ; short-range neighborlist cutoff (in nm)<br>rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm)<br>rvdw = 1.0 ; short-range van der Waals cutoff (in nm)<br>
; Electrostatics<br>coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics<br>pme_order = 4 ; cubic interpolation<br>fourierspacing = 0.16 ; grid spacing for FFT<br>; Temperature coupling is on<br>
tcoupl = V-rescale ; modified Berendsen thermostat<br>tc-grps = Protein Non-Protein ; two coupling groups - more accurate<br>tau_t = 0.1 0.1 ; time constant, in ps<br>ref_t = 250 250 ; reference temperature, one for each group, in K<br>
; Pressure coupling is off<br>pcoupl = no ; no pressure coupling in NVT<br>; Periodic boundary conditions<br>pbc = xyz ; 3-D PBC<br>; Dispersion correction<br>DispCorr = EnerPres ; account for cut-off vdW scheme<br>
; Velocity generation<br>gen_vel = yes ; assign velocities from Maxwell distribution<br>gen_temp = 250 ; temperature for Maxwell distribution<br>gen_seed = -1 ; generate a random seed<br><br>I did try to reduce the timestep from 2 fs to 1 fs but ran into the same error.<br>
<br><br><br>Searching through a few archives I got a hint it is something do to with water's density per cubic nm.<br>Is that whats going on here? <br>If yes, then how do I randomly delete some water molecules from my system?<br>
<br>Please help.<br><br>Thanks,<br>Shivangi<br><br><br><br><br><br>