Hi, all,<br><br>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?<br>
<br>Here is my mdp file:<br>title = OPLS Lysozyme NVT equilibration
<br>;define = -DPOSRES ; position restrain the protein
<br>; Run parameters
<br>integrator = bd ; leap-frog integrator
<br>nsteps = 500000 ; 2 * 500000 = 1000 ps
<br>dt = 0.002 ; 2 fs
<br>; Output control
<br>nstxout = 100 ; save coordinates every 0.2 ps
<br>nstvout = 100 ; save velocities every 0.2 ps
<br>nstenergy = 100 ; save energies every 0.2 ps
<br>nstlog = 100 ; update log file every 0.2 ps
<br>; Bond parameters
<br>continuation = yes ; first dynamics run
<br>constraint_algorithm = lincs ; holonomic constraints
<br>constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained
<br>lincs_iter = 1 ; accuracy of LINCS
<br>lincs_order = 4 ; also related to accuracy
<br>; Neighborsearching
<br>ns_type = grid ; search neighboring grid cells
<br>nstlist = 5 ; 10 fs
<br>rlist = 1.0 ; short-range neighborlist cutoff (in nm)
<br>rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm)
<br>rvdw = 1.0 ; short-range van der Waals cutoff (in nm)
<br>; Electrostatics
<br>coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics
<br>pme_order = 4 ; cubic interpolation
<br>fourierspacing = 0.16 ; grid spacing for FFT
<br>; Temperature coupling is on
<br>tcoupl = V-rescale ; modified Berendsen thermostat
<br>tc-grps = system ; two coupling groups - more accurate
<br>tau_t = 0.01 ; time constant, in ps
<br>ref_t = 400 ; reference temperature, one for each group, in K
<br>; Pressure coupling is off
<br>pcoupl = no ; no pressure coupling in NVT
<br>; Periodic boundary conditions
<br>pbc = xyz ; 3-D PBC
<br>; Dispersion correction
<br>DispCorr = EnerPres ; account for cut-off vdW scheme
<br>; Velocity generation
<br>gen_vel = yes ; assign velocities from Maxwell distribution changed
<br>gen_temp = 400 ; temperature for Maxwell distribution
<br>gen_seed = 100 ; generate a random seed
<br>ld_seed=-1
<br><br><br>Thank you!<br><br>Bo<br>