On 29/02/12, "bo.shuang" <[email protected]> wrote: > Hi, all, > > I have a question about change the temperature in simulation. When I change > the ref_t and gen_temp only, (from 300 to 400) I cannot see any difference. I > am thinking if I need to change tau_t also, since diffusivity constant is > also related to temperature. Am I right? > > Here is my mdp file: > title = OPLS Lysozyme NVT equilibration > ;define = -DPOSRES ; position restrain the protein > ; Run parameters > integrator = bd ; leap-frog integrator
By their nature, Browning and stochastic dynamics do not work with temperature coupling algorithms. IIRC gen_temp + gen_vel should have an effect on the initial conditions. Mark > > > nsteps = 500000 ; 2 * 500000 = 1000 ps > dt = 0.002 ; 2 fs > ; Output control > nstxout = 100 ; save coordinates every 0.2 ps > nstvout = 100 ; save velocities every 0.2 ps > nstenergy = 100 ; save energies every 0.2 ps > nstlog = 100 ; update log file every 0.2 ps > ; Bond parameters > continuation = yes ; 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 cells > nstlist = 5 ; 10 fs > rlist = 1.0 ; short-range neighborlist cutoff (in nm) > rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm) > rvdw = 1.0 ; 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 = system ; two coupling groups - more accurate > tau_t = 0.01 ; time constant, in ps > ref_t = 400 ; 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 > changed > gen_temp = 400 ; temperature for Maxwell distribution > gen_seed = 100 ; generate a random seed > ld_seed=-1 > > > Thank you! > > Bo > >
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