# HG changeset patch # User fmercuri # Date 1624475003 0 # Node ID 434ecf9668fa5d80ec570881f3349e1c97d2625e # Parent e9350579a698b8bab4ef960380bec659d91f5a69 Uploaded diff -r e9350579a698 -r 434ecf9668fa npt.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/npt.xml Wed Jun 23 19:03:23 2021 +0000 @@ -0,0 +1,180 @@ + + - constant-temperature and -pressure equilibration of a system + + macros.xml + + + + + > verbose.txt && + gmx mdrun -deffnm npt &>> verbose.txt + + #if $str == 'pdb' or $str == 'both' + && gmx editconf -f npt.gro -o npt.pdb &>> verbose.txt + #end if + + ]]> + + + + #if $mdp.mdpfile == 'default': + title = NPT equilibration + define = -DPOSRES ; position restrain the protein + ; Run parameters + integrator = $mdp.integrator ; leap-frog integrator + nsteps = $mdp.md_steps ; 2 * 50000 = 100 ps + dt = $mdp.step_length ; 2 fs + ; Output control + nstxout = $mdp.write_freq ; save coordinates every 1.0 ps + nstvout = $mdp.write_freq ; save velocities every 1.0 ps + nstenergy = $mdp.write_freq ; save energies every 1.0 ps + nstlog = $mdp.write_freq ; update log file every 1.0 ps + nstxout-compressed = $mdp.write_freq ; save compressed coordinates every 10.0 ps + + ; Bond parameters + continuation = yes ; Restarting after NVT + constraint_algorithm = lincs ; holonomic constraints + constraints = $mdp.constraints ; all bonds (even heavy atom-H bonds) constrained + lincs_iter = 1 ; accuracy of LINCS + lincs_order = 4 ; also related to accuracy + ; Neighborsearching + cutoff-scheme = $mdp.cutoffscheme + ns_type = grid ; search neighboring grid cells + nstlist = 10 ; 20 fs, largely irrelevant with Verlet scheme + rcoulomb = $mdp.rcoulomb ; Short-range electrostatic cut-off + rlist = $mdp.rlist ; Cut-off distance for the short-range neighbor list. + rvdw = $mdp.rvdw ; Short-range Van der Waals cut-off + ; Electrostatics + coulombtype = $mdp.coulombtype ; method for electrostatics calculations e.g. PME + pme_order = 4 ; cubic interpolation + fourierspacing = 0.16 ; grid spacing for FFT + ; Temperature coupling is on + tcoupl = V-rescale ; modified Berendsen thermostat + tc-grps = Protein Non-Protein ; two coupling groups - more accurate + tau_t = 0.1 0.1 ; time constant, in ps + ref_t = $mdp.temperature $mdp.temperature ; reference temperature, one for each group, in K + ; Pressure coupling is on + pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT + pcoupltype = isotropic ; uniform scaling of box vectors + tau_p = 2.0 ; time constant, in ps + ref_p = $mdp.refp ; reference pressure, in bar + compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1 + refcoord_scaling = com + ; Periodic boundary conditions + pbc = xyz ; 3-D PBC + ; Dispersion correction + DispCorr = EnerPres ; account for cut-off vdW scheme + ; Velocity generation + gen_vel = no ; Velocity generation is off + #end if + + + + + + + + + + + + + + str == 'gro' or str == 'both' + + + str == 'pdb' or str == 'both' + + + + traj == 'trr' or traj == 'both' + + + traj == 'xtc' or traj == 'both' + + + capture_log + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +