Re: [AMBER] Protein drift from solvent box

From: Lizelle Lubbe <>
Date: Thu, 19 Oct 2017 14:58:51 +0000

Hi Bill,

Thanks for the reply. Not sure I understand what you mean though.
I did not intentionally set the cut value in<> and<> equal to the distance between the glycans and solvent boundary. 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.

Could you please explain to me why this is incorrect and how it would cause shrinkage of the box?

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?

From: Bill Ross <<>>
Sent: Donderdag, Oktober 19, 2017 4:29 nm.
Subject: Re: [AMBER] Protein drift from solvent box
To:<> <<>>

The box size should not be used as the cutoff, if that's what you did.
The box will shrink and the cutoff will extend beyond it, not sure what
the consequences are anymore.


On 10/19/17 7:06 AM, Thakur, Abhishek wrote:
> I have solvated my glycoprotein using the tleap input file given below. It specified that the distance between solute and boundary should be 10.0 and, assuming that this was the case, I proceeded to use this as input for MD.

AMBER mailing list<>

Disclaimer - University of Cape Town This e-mail is subject to UCT policies and e-mail disclaimer published on our website at or obtainable from +27 21 650 9111. If this e-mail is not related to the business of UCT, it is sent by the sender in an individual capacity. Please report security incidents or abuse via
AMBER mailing list
Received on Thu Oct 19 2017 - 08:00:02 PDT
Custom Search