Re: [AMBER] Protein drift from solvent box

From: Lizelle Lubbe <>
Date: Thu, 19 Oct 2017 16:14:32 +0000

Thanks David, I will try autoimage again and report back.
Just to clarify, do you mean 10A is rather short for the solvent-solute barrier or non-bonded distance?
From: David A Case <<>>
Sent: Donderdag, Oktober 19, 2017 6:11 nm.
Subject: Re: [AMBER] Protein drift from solvent box
To: AMBER Mailing List <<>>

On Thu, Oct 19, 2017, Lizelle Lubbe wrote:

I thought that 10A was commonly used for the non-bonded cutoff distance
and to avoid the computational cost of extra waters I chose 10A instead of
12A for the barrier distance.

10 Ang is pretty short; 12-14 Ang would be some better, but that's mostly a
recommendation for future work, i.e. you probably don't need to re-do the
simulations you already have.
> Could you please explain to me why this is incorrect and how it would
> cause shrinkage of the box?

What you did sounds fine.

> I measured the glycan-glycan distance between neighbouring periodic
> images after 8ns production and during the simulation it ranges between
> 25-70A. Does this mean that the protein drift is just an imaging issue
> or can the molecules start interacting later on?

The protein drift should be just an imaging problem. See if running autoimage
followed visualization looks OK.


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Received on Thu Oct 19 2017 - 09:30:05 PDT
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