Dear users, I am using the Reaction-Field method for electrostatics interactions. I used the following parameters for all input files (em.mdp, pr.mdp, nvt.mdp, npt.mdp, md.mdp). I just changed as an epsilon_rf=78 in md.mdp. If I set nstlist=rlist=rcoulomb=rvdw=1.0 for energy minimization, would not it be better? What is your suggestions?
; Neighbor Searching Parameters nstlist = 5 ns-type = Grid pbc = xyz rlist = 0.9 ; Electrostatics coulombtype = Reaction-Field rcoulomb = 1.4 epsilon_rf = 54 ; VdW vdw-type = Cut-off rvdw = 1.4 * Another question:* I used 200 K (in pr.mdp) and 300 K (in nvt.mdp, npt.mdp and md.mdp) the reference temperature for coupling. I analysed the temperature after production run. I get "Temperature=312.646" (g_energy -f md.edr -o temperature.xvg). that is, The temperature has increased (approximately 12 K) during the simulation. What could be the reason for the increase in temperature? I had setted to 200 K the reference temperature for coupling in pr.mdp. it can cause? My em.mdp file is as the following: *em.mdp:* title = Energy Minimization ; Title of run cpp = /lib/cpp ; Preprocessor: Line tell the program the standard locations where to find certain files define = -DFLEXIBLE ; defines to pass to the preprocessor ; Run Control integrator = steep ; steep integrator (steep = steepest descent minimization) nsteps = 2500 ; maximum number of steps to integrate ; Energy Minimization emtol = 1000.0 ; [kJ/mol/nm] minimization is converged when max force is < emtol emstep = 0.01 ; [nm] initial step-size ; Output Control nstxout = 0 ; [steps] freq to write coordinates to trajectory nstvout = 0 ; [steps] freq to write velocities to trajectory nstfout = 0 ; [steps] freq to write forces to trajectory nstlog = 1 ; [steps] freq to write energies to log file nstenergy = 1 ; [steps] freq to write energies to energy file energygrps = System ; group(s) to write to energy file ; Neighbor Searching Parameters nstlist = 5 ; [steps] freq to update neighbor list ns-type = Grid ; method of updating neighbor list pbc = xyz ; periodic boundary conditions (yes/no)in all directions rlist = 0.9 ; [nm] cut-off distance for the short-range neighbor list ; Electrostatics coulombtype = Reaction-Field ; Reaction-Field electrostatics rcoulomb = 1.4 ; [nm] distance for Coulomb cut-off epsilon_rf = 54 ; The relative dielectric constant of the reaction field ; VdW vdw-type = Cut-off ; twin-range cut-off with rlist where rvdw >= rlist rvdw = 1.4 ; [nm] distance for LJ cut-off ; Bonds constraints = none ; convert all bonds to constraints -- Ahmet Yıldırım
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