Dear Gromacs users, I have made an initial system with a number of molecules in a "large" box.
Large means a box of size 50 50 50 nm? I am interested in the self-assembly process of molecules (parametrized in charmm36 ff) in the box. I expected pressure coupling to shrink the box quickly, but it seems it fails to do so. The simulation box did not change (ca. 0.5 nm in each direction) which seems strange to me. I have used four different P-couple schemes for 4 different type of self-assemblies: 1) isotropic pcoupl = berendsen pcoupltype = isotropic tau_p = 5.0 compressibility = 4.5e-5 ref_p = 1.0 2) semiisotropic pcoupl = berendsen pcoupltype = semiisotropic tau_p = 5.0 compressibility = 4.5e-5 4.5e-5 ref_p = 1.0 1.0 3) anisotropic with *fix shape* of box (*but the size could change*) pcoupl = berendsen pcoupltype = anisotropic tau_p = 5.0 compressibility = 4.5e-5 4.5e-5 4.5e-5 0 0 0 ref_p = 1.0 1.0 1.0 0 0 0 4) anisotropic with *both size and shape able to change* pcoupl = berendsen pcoupltype = anisotropic tau_p = 5.0 compressibility = 4.5e-5 4.5e-5 4.5e-5 4.5e-5 4.5e-5 4.5e-5 ref_p = 1.0 1.0 1.0 0 0 0 Here are some other parameters in mdp file which might be useful for finding the problem: integrator = md dt = 0.002 nsteps = 50000 nstlog = 1000 nstxout = 1000 nstvout = 1000 nstfout = 1000 nstcalcenergy = 100 nstenergy = 1000 cutoff-scheme = Verlet nstlist = 20 rlist = 1.2 coulombtype = pme rcoulomb = 1.2 vdwtype = Cut-off vdw-modifier = Force-switch rvdw_switch = 1.0 rvdw = 1.2 tcoupl = berendsen tc_grps = Molecules water_ions tau_t = 1.0 1.0 ref_t = 355 355 constraints = h-bonds constraint_algorithm = LINCS continuation = yes nstcomm = 100 comm_mode = linear comm_grps = Molecules WI refcoord_scaling = com gen-vel = no I can make the initial system smaller, but I think starting from a large box would be better because it gives all the molecule enough freedom to move and assemble in better way. Is not it right to expect the p-couple shrink the box in nanoseconds? This was only for 100 ps but I expected more shrinkage of box. What do you think? Thanks in advance for your comments Cheers Mohsen -- *Rewards work better than punishment ...* -- *Rewards work better than punishment ...* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to [email protected].
