Dear all, I'm doing a simulation of the formation of a lipid monolayer, and my system contains a water layer on the bottom and a layer of the mixture of lipid and decane on the top. Since I expect the pbc to be only applied to the x and y direction, I then decide to use the method of "walls".
However, I'm not sure what exactly is the function of the walls? Do they prevent the two adjacent boxes from interacting with each other completely? Moreover, as mentioned in the manual, if I use "ewald_geometry = 3dc", I can try to increase the z-dimension of the box, usually by 3 times the dimension in the z direction. Since the walls are set up in the mdp file which is applied to the extended box, then I suppose the walls would be located at the bottom and top of the extended box rather than the original box, aren't they? in other words, the molecules will go to the extended region of the box in stead of staying in the original box, am I correct? So do I still need to extend the box if I'm going to use walls? Finally, in order to perform the 2 dimensional simulation, do I need to modify all the mdp files for EM, NVT, NPT and MD, where the "pbc" term is changed to "pbc=xy" and the options for walls are specified? I've attached my mdp file for MD below. Sorry for raising so many questions. Could any one kindly help me with this? I would very much appreciate it! Thanks a lot! Clare title = Lipid decane and water ; Run parameters integrator = md ; leap-frog integrator nsteps = 5000000 ; 2 *5000000 = 50000 ps, 10 ns dt = 0.002 ; 2 fs ; Output control nstxout = 1000 ; save coordinates every 2 ps nstvout = 1000 ; save velocities every 2 ps nstxtcout = 1000 ; xtc compressed trajectory output every 2 ps nstenergy = 1000 ; save energies every 2 ps nstlog = 1000 ; update log file every 2 ps ; Bond parameters continuation = yes ; Restarting after NPT 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 = 10 ; 10 fs rlist = 0.9 ; short-range neighborlist cutoff (in nm) rcoulomb = 0.9 ; short-range electrostatic cutoff (in nm) rvdw = 0.9 ; 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 optimize_fft = yes ; optimize at startup for faster long sims ewald_geometry = 3dc ; Ewald sum in 2Ds ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = Lipid SOL Decane ; two coupling groups - more accurate tau_t = 0.1 0.1 0.1 ; time constant, in ps ref_t = 300 300 300; 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 = 1.0 ; reference pressure, in bar compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1 ; Periodic boundary conditions pbc = xy ; 2-D PBC ; Dispersion correction DispCorr = EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = no ; Velocity generation is off ; walls nwall = 2 wall_atomtype = SOL C10 ;wall at z=0 is formed by water and at z=z_box is formed by decane wall_type = 9-3 ; ;wall_r_linpot = 0 ; wall_density = 33.3679 3.0897; number density of water and decane wall_ewald_zfac = 3 ; -- View this message in context: http://gromacs.5086.n6.nabble.com/configurations-of-the-two-dimensional-simulation-tp5000833.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
