On 3/28/13 8:25 PM, Peter Eastman wrote:
After further study of the documentation, I find myself getting more confused rather than
less. I see that the [pairs] and [pairtypes] directives only specify LJ parameters, not
Coulomb parameters. (There's a function type 2 for [pairs] that does include charges,
but the manual says that function type is only used for free energy calculations.) How
do I select the latter when gen-pairs is off? Is it simply assumed that 1-4 Coulomb
interactions are never reduced for force fields that don't use gen-pairs? Table 5.5
lists an alternate directive, [pairs_nb] that does specify Coulomb parameters as well as
LJ. But no other mention of this directive appears anywhere else in the manual, there
doesn't seem to be any corresponding [pairtypes] option, and a grep reveals that
"pairs_nb" never occurs in any file in the entire top directory.
What am I misunderstanding?
Which version of the manual are you using? I recall the discussion on
[pairs_nb] being absent in an older version, but manual section 5.3.4 in version
4.6.1 has lots of discussion on [pairs_nb].
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
