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].
I was looking at the 4.5.3 manual. I just downloaded the 4.6.1 manual, and I
see it now
Ok, thanks.
Peter
On Mar 29, 2013, at 10:22 AM, Justin Lemkul jalem...@vt.edu wrote:
On Fri, Mar 29, 2013 at 1:16 PM, Peter Eastman peast...@stanford.eduwrote:
Which version of the manual are you using? I recall the discussion on
[pairs_nb] being absent in an older version, but manual
).
Is that correct?
Thanks!
Peter
On Mar 28, 2013, at 4:20 AM, Justin Lemkul jalem...@vt.edu wrote:
On 3/27/13 5:12 PM, Peter Eastman wrote:
I'm implementing a TOP file reader, and I have a question about an ambiguity
in the format. The [ pairs ] block lists atom pairs that should
3. If gen-pairs is yes, then generate parameters for all 1-2, 1-3, and 1-4
pairs for which we did not already find parameters in step 1 or 2 (regardless
of whether or not a [pairs] line exists for a particular pair).
Or rather, generate an [exclusions] record for each 1-2 and 1-3, and a
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
I'm implementing a TOP file reader, and I have a question about an ambiguity in
the format. The [ pairs ] block lists atom pairs that should be handled
specially (exclusions and 1-4 interactions). In addition, the gen-pairs flag
can indicate that pairs are generated automatically. But all
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