Hi Bill,
Thanks for the reply. Not sure I understand what you mean though.
I did not intentionally set the cut value in min.in<
http://min.in> and prod.in<
http://prod.in> 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?
Lizelle
_____________________________
From: Bill Ross <ross.cgl.ucsf.edu<mailto:ross.cgl.ucsf.edu>>
Sent: Donderdag, Oktober 19, 2017 4:29 nm.
Subject: Re: [AMBER] Protein drift from solvent box
To: amber.ambermd.org<mailto:amber.ambermd.org> <amber.ambermd.org<mailto:amber.ambermd.org>>
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.
Bill
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.
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Received on Thu Oct 19 2017 - 08:00:02 PDT
