Hi Gromacs Friends,<br> <br>I planed to do simulated annealing...<br>My protocol is as follow <br>( forcefield G96 53a6 spc water model)<br><br>1. nvt at 310 k for 100 ps <br>2. Sa (mdp is posted below )<br>3. NPT at 310 k for 100 ps <br>
<br>Is it right ??<br><br>Please suggest me improvements...<br><br>Sa mdp file <br><br>title = gromacs<br>define = -DPOSRES ; position restrain the protein<br><br>nstcomm = 1<br>comm-mode = Linear; Run parameters<br>
integrator = md ; leap-frog integrator<br>nsteps = 500000 ; 2 * 50000 = 100 ps<br>dt = 0.002 ; 2 fs<br>; Output control<br>nstxout = 1000 ; save coordinates every 0.2 ps<br>
nstvout = 1000 ; save velocities every 0.2 ps<br>nstenergy = 1000 ; save energies every 0.2 ps<br>nstlog = 1000 ; update log file every 0.2 ps<br>; Bond parameters<br>continuation = yes ; Restarting after NVT <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 = 0.9 ; short-range neighborlist cutoff (in nm)<br>rcoulomb = 0.9 ; short-range electrostatic cutoff (in nm)<br>
vdw-type = Cut-off<br>rvdw = 1.4 ; 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 = Protein Non-Protein ; two coupling groups - more accurate<br>
tau_t = 0.1 0.1 ; time constant, in ps<br>ref_t = 310 310 ; reference temperature, one for each group, in K<br>; Pressure coupling is on<br>pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT<br>
pcoupltype = isotropic ; uniform scaling of box vectors<br>tau_p = 2.0 ; time constant, in ps<br>ref_p = 1.0 ; reference pressure, in bar<br>compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1<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 = no ; Velocity generation is off <br>
; Simulated annealing<br>annealing = single single<br>annealing_npoints = 4 4<br>annealing_time = 0 200 400 600 0 200 400 600 <br>annealing_temp = 310 323 300 310 310 323 300 310 <br>
<br><br><br><br>Thank you in advance <br><br>With Best Wishes,<br>Rama David <br>