Hello to all dear gromacs users I'm simulating a monolayer using pcouple= surface tension and as manual says my converged area per lipid and surface tension are very much dependable on the value of tau-p , so can some one help me how can I make sure that my tau-p value is OK? thanks Ali mdp script: ; Run parameters integrator = md ; leap-frog integrator nsteps = 5000000 ; (10 ns) dt = 0.001 ; 1 fs ; Output control nstxout = 100000 ; save coordinates every 0.2 ps nstvout = 100000 ; save velocities every 0.2 ps nstenergy = 500 ; save energies every 0.2 ps nstlog = 1000 ; update log file every 0.2 ps ; Bond parameters continuation = yes ; Restarting after NVT 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 cutoff-scheme = Verlet ns_type = grid ; search neighboring grid cels nstlist = 10 ; 10 fs rlist = 1.4 ; short-range neighborlist cutoff (in nm) rcoulomb = 1.4 ; short-range electrostatic cutoff (in nm) rvdw = 1.4 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation vdwtype = Cut-off ; Temperature coupling is on tcoupl = berendsen ; More accurate thermostat tc-grps = SOL OCT ; three coupling groups - more accurate tau_t = 0.5 0.5 ; time constant, in ps ref_t = 300 300 ; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl = berendsen ; Pressure coupling on in NPT pcoupltype = surface-tension ; uniform scaling of x-y box vectors, independent z tau_p = 1.0 1.0 ; time constant, in ps ref_p = 800 1.0 ; reference pressure, x-y, z (in bar) compressibility = 4.5e-5 0 ; isothermal compressibility, bar^-1 ; 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 ; COM motion removal ; These options remove motion of the protein/bilayer relative to the solvent/ions nstcomm = 10 comm-mode = Linear comm-grps = SOL OCT -- Gromacs Users mailing list
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