Re: [AMBER] Sander bomb: how to create a larger box

From: Ruth Helena Tichauer <>
Date: Tue, 2 Aug 2016 16:14:33 +0200

Dear David,

By two months I mean: I’ve been running this QM/MM simulation for two months now. As water molecules in the active site of my protein are part of the QM region and as they diffuse away, I have to regularly take into account this exchange in my mdin file which takes some time.. So, if in order to have a bigger box I’d have to start my simulation all over from 0 ps, I’d be loosing two months of work..

Thank you for your suggestion,


> On 01 Aug 2016, at 16:57, David A Case <> wrote:
> On Mon, Aug 01, 2016, Ruth Helena Tichauer wrote:
>> It would save me two months' work so I guess I’ll try this out and I
>> hope it will work without a huge bias of the results..
> Why two months? Generally you should equilibrate the new water box using
> MM alone (perhaps with restraints to keep what used to be the QM part fixed.)
> Then, go back to the QM/MM calculations.
> ...dac
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Received on Tue Aug 02 2016 - 07:30:02 PDT
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