[gmx-users] User-defined potentials and meaning of table extension

Justin Lemkul jalemkul at vt.edu
Fri Mar 21 11:28:26 CET 2014

On 3/21/14, 5:22 AM, Davide Mercadante wrote:
> Hello GMX users,
> I am testing the use of User-defined on a box of water and I came across
> the issue of table-extension option.
> I don't understand the use of it. If I specify a cutoff of 1 nm and then
> give a table extension of 0 nm then the cutoff will be 1 nm otherwise it
> will be cutoff+table-extension value. This is pretty clear. However, it is
> not clear why a table extension is needed.

The value of table-extension does not modify the cutoff.  You need to specify 
values beyond rc for proper bookkeeping of nonbonded interactions.  So if rc is 
1.0 in the .mdp file, it's a good idea to write the table out to 2.0 nm to be in 
line with table-extension = 1, the default value.

> As a test, I have run this on only two water molecules placed at a distance
> within the cutoff coupled to table-extension = 0nm and to table-extension =
> 1 nm.
> In both cases, the values listed in the table seem to be considered up to
> the cut-off and the table extension seem to be ignored?
> A puzzling thing that happened is that then, for a box of water (216
> molecules), using table extension = 0 nm (cutoff 0.5 nm) I get an unstable
> and crashing simulation, while if I use table extension = 1 nm (cutoff 0.5
> nm) the system runs smoothly.
> Can you please help me to understand this?

Using an extension of zero probably leads to missing interactions.  Note the 
second sentence of the table-extension explanation in the manual tells you why 
it is needed.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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