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

Andrew Mauro andrewkmauro at gmail.com
Fri Mar 11 18:59:33 CET 2011

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
The simulation was run using GROMACS 4.5 with the amber96ff with brownian
– 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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