[gmx-users] Implicit Solvent seems to collapse molecule to origin

[Andrew Mauro]

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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