[gmx-users] Determining the cut offs more than half of the box

Justin Lemkul jalemkul at vt.edu
Sun Nov 19 18:05:59 CET 2017

On 11/19/17 3:17 AM, Iman Ahmadabadi wrote:
> Dear Mr.Mark Abraham,
> Thank you for your help.
> Because of the accuracy of the results, I should use a reasonable cut offs
> for the interactions around 2.0 nm. The cut offs less than 1.0 nm are too
> small for my project because of the importance of long range interactions.

What force field are you using? I know of none that require a 2.0-nm 
cutoff. Note that longer cutoffs do not necessarily provide you with 
greater accuracy (in fact, it can make results worse, depending on the 
force field and the components of the system).

> The box size is an obstacle to determining the desired cut off for
> interactions.

What you're fighting against is the minimum image convention - the 
shortest box vector must be at least twice as large as the longest 
cutoff to avoid double-counting of forces. If you have a convincing 
reason to use a 2.0-nm cutoff, then the absolute minimum size your box 
must be is 4.0 nm in all directions, but you should construct a box 
larger than that if using pressure coupling, because fluctuations in 
pressure can cause the box size to decrease. If you go below 4.0 nm 
exactly, mdrun will fail.



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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