Re: [AMBER] Simulating pyridine in water TIP3P

From: David A Case <>
Date: Thu, 28 May 2020 21:33:01 -0400

On Thu, May 28, 2020, Debarati DasGupta wrote:

>I faced this error in equilibration step. Should I have a smaller cut value?
>Cutoff list exceeds largest sphere in unit cell!!

No: you need to have a bigger system. When a side of the periodic box
gets to be less than about 20 Ang., it gets to be too small for Amber to
handle, since Amber was designed and optimized for larger periodic

You may be able to get away with setting skinnb to 1 (instead of its
default value of 2). That will allow you to go to slightly smaller
boxes. But it would be rather dangerous to reduce the cutoff value to
anything below 8 Ang: we cut off Lennard-Jones interactions at "cut",
and 8 Ang. is already on the edge of being to small.

By far the simplest fix is to just use more water molecules in your
original setup.


AMBER mailing list
Received on Thu May 28 2020 - 19:00:02 PDT
Custom Search