Remove water to close to the protein?

From: Per Jr. Greisen (
Date: Fri May 26 2006 - 07:59:27 CDT


I have solvated my protein and during my minimization I have a lot of
spikes in the beginning - to around 500 steps. My question is:

1. How to remove the waters that are placed too close to the protein

2. And is it possible to identify the spikes from the minimization?

Thanks in advanced

Best Regards
Per Jr. Greisen

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