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I am trying to simulate a protein-RNA complexed with a ligand where the ribonucleotide residues of which the total charges is -1 in the CHARMM36 force-field which makes the whole RNA protein complex highly negative (about -224) and to neutralize the system Sodium(Na+) was used as counter-ions and when the system is made to undergo dynamics with all of the biomolecule positionally restrained, these counter-ions which before equilibration were fine,these Na+ ions swims near the ligand and this phenomenon happens when Particle Mesh Ewald(PME) is used to calculate long range interactions but these same ions(Na+) don’t swim near the ligand when plain cut-off is used. Can there be some other way round where I can read these RNA residues as neutral residues such that I don’t need to add this many number of counter-ions which influence my ligand with that high number of positive charges. I have checked in the CHARMM force field such rtp entries for neutral residues are not provided and the residues which are there are only for the Nitrogenous bases.
These are the contents of my mdp file:
title = NVT equilibration define = -DPOSRES ; position restrain the protein ; Run parameters integrator = md ; leap-frog integrator nsteps = 2500000 ; 2 * 2500000 = 5000 ps (5ns) dt = 0.002 ; 2 fs ; Output control nstxout = 500 ; save coordinates every 1.0 ps nstvout = 500 ; save velocities every 1.0 ps nstenergy = 500 ; save energies every 1.0 ps nstlog = 500 ; update log file every 1.0 ps ; Bond parameters continuation = no ; first dynamics run constraint_algorithm = lincs ; holonomic constraints constraints = h-bonds ; bonds involving H are constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Nonbonded settings cutoff-scheme = Verlet ; Buffered neighbor searching ns_type = grid ; search neighboring grid cells nstlist = 10 ; 20 fs, largely irrelevant with Verlet rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm) rvdw = 1.0 ; short-range van der Waals cutoff (in nm) DispCorr = EnerPres ; account for cut-off vdW scheme ; 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 Non-Protein ; two coupling groups 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 ; 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 RNA residues are as such attached here:
Thanking in advance.
Kindly do send in your suggestions.