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

[Justin Lemkul]

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

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

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