AMBER Archive (2006)

Subject: Re: AMBER: puzzles about solvatoct or solvatebox

From: Zhihong Yu (computation_at_mail.nankai.edu.cn)
Date: Tue Oct 17 2006 - 09:42:54 CDT

Dear Bill,

thanks for your response!

>> I found that the solute is not in the center of oct-box
>
>It sounds like there is a bug in solvateoct.
>
Is it really a bug or not? in MD simulations, the solute must be placed in the center of the (oct)box? or just being completely buried in the solvent is OK? if the latter is YES, then I'll just increase the buffer to 12 to completely solvate my system with the cost of more 2400 waters.

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