HI , Dear Gromacs Users, I´ve been trying to run a NVT simulation, in order to equilibrate my system( POPC + IONCHANNEL + SOL_IONS and DOX( Drug Molecule), i have already run a EM, with DFLEXIBLE, and when i´m trying to run the NVT.mdp, the usual comment of Water cannot be settle appear
and this Step 1, time 0.002 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 417295953701.842102, max 94388491386880.000000 (between atoms 7122 and 7123) bonds that rotated more than 30 degrees: according with previous post, this could be of a problem of the topol (DOX) or problems with my mdp file, this is my .mdp , i was wondering if you could help me and give me some advices to solve this Thanks in advance for your time and attention , Andres Ortega title = NVT equilibration for channel_dox define = -DPOSRES -DPOSRES_DOX ; position restrain the protein and for DOX ; Run parameters integrator = md ; leap-frog integrator nsteps = 5000000 ; 2 * 500000 = 1 ns ;10ns dt = 0.002 ; 2 fs cutoff-scheme = verlet ; ; Output control nstxout = 1000 ; save coordinates every 2 ps nstvout = 1000 ; save velocities every 2 ps nstenergy = 1000 ; save energies every 2 ps nstlog = 1000 ; update log file every 2 ps ; 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 cels nstlist = 10 ; 10 fs rlist = 1.2 ; short-range neighborlist cutoff (in nm) rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm) rvdw = 1.2 ; 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 is on tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = Protein POPC DOX Water_and_ions ; three coupling groups - more accurate tau_t = 0.1 0.1 0.1 0.1 ; time constant, in ps ref_t = 310 310 310 310 ; 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 ; Dispersion correction DispCorr = EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = yes ; assign velocities from Maxwell distribution gen_temp = 310 ; temperature for Maxwell distribution gen_seed = -1 ; generate a random seed ; COM motion removal ; These options remove motion of the protein/bilayer relative to the solvent/ions nstcomm = 1 comm-mode = Linear comm-grps = Protein_POPC DOX Water_and_ions -- View this message in context: http://gromacs.5086.x6.nabble.com/NVT-problem-tp5015174.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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 [email protected].
