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 -- ================================================== 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 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul ================================================== -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
