Hello, I got a problem, trying to make preparation (in particular, heating from 0 to 300 K) of my system in implicit solvent (GBSA OBC model). For gradual heating I use simulated annealing (see mdp below) and sd integrator, which allows me do not use thermostat. I also set up gen_vel = yes and gen_temp = 0 (I am not sure, is it correct way or not). The problem appears: on the 0th step in output line temperature is ~305 K and it drops to ~8 K during 0.7 ps of simulation after that it starts to fluctuate around constant value (~ 10 K). At the beginning in output file there is line 'Initial temperature: 0 K', but started mdrun shows temperature 305 K. At the same time 'Current ref_t for group System' changes correctly step by step. I did try different parameters (turn on thermostat, turn off annealing, set gen_vel 0 or 300 K) - the same story. My guess is the problem with minimization. Algorithm "steepest descent" had convergent for 300 steps (in spite of very low emtol which I set up) and total potential energy dropped to constant minimum, I recompiled gromacs with double precision but minimization result was the same. Looks like my system (it's ~400000 atoms) fell in some local minimum which gives me high initial temperature. What is wrong? Or it's proper behavior? Does it matter that I use cut-offs? Here is mdp file: define = -DFLEXIBLE constraints = none integrator = sd dt = 0.001; 1fs nsteps = 300000 ; 300 ps nstcomm = 1 nstxout = 1000 ; frequency to write coordinates to output trajectory nstvout = 0 ; frequency to write velocities to output trajectory; the last velocities are always written nstfout = 0 ; frequency to write forces to output trajectory nstlog = 10 ; frequency to write energies to log file nstenergy = 100 ; frequency to write energies to edr file nstcalcenergy = 100 vdwtype = cut-off coulombtype = cut-off pbc = no table-extension = 20.0 nstlist = 100 ns_type = grid rlist = 1.0 rcoulomb = 1.1 rvdw = 1.1 comm-mode = angular comm-grps = system optimize_fft = yes ;heating annealing = single annealing_npoints = 2 annealing_time = 0 300 annealing_temp = 0 300 ld_seed = 8072012 ; V-rescale temperature coupling is on Tcoupl = no tau_t = 0.02 tc_grps = system ref_t = 0 ; Pressure coupling is off Pcoupl = no ; Generate velocites is on gen_vel = yes gen_temp = 0 gen_seed = 8042012 ; Implicit solvent implicit_solvent = GBSA gb_algorithm = OBC; Still ; HCT ; OBC nstgbradii = 1 rgbradii = 1.0 ; [nm] Cut-off for the calculation of the Born radii. Currently must be equal to rlist gb_epsilon_solvent = 80 ; Dielectric constant for the implicit solvent sa_algorithm = Ace-approximation sa_surface_tension = -1 I will be very appreciated for any help. - Olga Kononova
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