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.
Mark
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