set the cross-sigma parameter for water-pocket to an unphysically large
value.
On Fri, Oct 30, 2015 at 4:20 AM, fjliu <fjliu.itcs.ecnu.edu.cn> wrote:
> Dear all,
>
> Are there any methods to prevent the water molecules entering into
> the binding pocket during the MD simulation? Can the hardwall constraint
> be used and how? I want to know this because I have a system with a
> crystal water resides stably in the binding pocket as it has hydrogen
> bonds formed with both the ligand and protein residue, I want to do a MD
> simulation with removing this water and preventing any other waters
> getting in.
>
> Thanks for your help!
> Best wishes! Fengjiao
>
>
>
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Received on Fri Oct 30 2015 - 04:00:04 PDT
