Hi, While running a simulation of capped alanine in an implicit solvent the molecule appears to collapse on itself such that the atoms have coordinates of 0,0,0 or some even have NaN. Has anyone else had this problem or any suggestions? The simulation was run using GROMACS 4.5 with the amber96ff with brownian dynamics. Parameters – Langevin dynamics = bd – Bd_fric= 95 [amu ps^-1] – Implicit_solvent= GBSA – gb_altorithm= OBC – gb_epsilon_solvent = 80 (dielectric constant of H20) – Sa_surface_tension = 2.092 [kJ mol^-1 nm^-2 ] – Thermostat= vscale
Thanks for any help. -- Andrew Mauro
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