[gmx-users] Re: Implicit solvent problems

Mark Abraham Mark.Abraham at anu.edu.au
Thu Oct 13 15:46:40 CEST 2011

On 14/10/2011 12:38 AM, liaoxyi wrote:
> Dear all,
> Thank you for giving me some hints for my problems.
> The problems has been solved now, the key is
> to adjust the gb_dielectric_offset to a smaller value like 0.05,
> then the /minimization /gets going normally.

You should use the value recommended for the model you are implementing 
- the default is suitable for the models in GROMACS.

> Subsequently, the NVT goes well.
> Still, I don't quite understand what role
> the gb_dielectric_offset actually plays ?

You will need to read some literature here - and should have done before 
changing the default values :-). I suggest starting with the OBC paper 
referenced in the manual.

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