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