On 3/27/17 4:12 PM, Graziele Bortolini wrote:
When I tried to do a thermalization for a PSB molecule (it has 66 atoms), in vacuum, the molecule rotate around the center of mass. This's my .mdp file: ------------------- cpp = /lib/cpp integrator = md dt = 0.001 nsteps = 500000 nstcomm = 1 nstxout = 0 nstvout = 0 nstlog = 0 nstenergy = 50 nstxtcout = 50 energygrps = PSB nstlist = 10 ns_type = grid rlist = 0.4 coulombtype = Cut-off optimize_fft = yes rcoulomb = 0.8 vdwtype = shift rvdw = 0.8 tcoupl = berendsen tc_grps = system ref_t = 300.0 tau_t = 0.1 pcoupl = berendsen ref_p = 1.000 compressibility = 4.5e-5 tau_p = 1.0 pcoupltype = isotropic gen_vel = yes gen_temp = 300.0 pbc = xyz ------------------- So, I tried to put the "comm-mode = angular", it supposedly remove center of mass translation and rotation. But when I do it I receive the following message: "WARNING 1 : Removing the rotation around the center of mass in a periodic system, this can lead to artifacts. Only use this on a single (cluster of) molecules. This cluster should not cross periodic boundaries." What I'm doing wrong?
You're not running in vacuo. By using finite cutoffs and using PBC, you're simulating a molecule in some sparsely populated pseudocrystalline state. To run in vacuo, set all cutoffs to zero (which means infinite), use no PBC, and set comm-mode = angular.
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