On 3/28/13 7:14 PM, Peter Eastman wrote:
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 [pairs]
record for each 1-4.
Not quite. The presence of an entry in [pairs] is required. When processing
the topology, grompp doesn't do any magic. It won't generate pair interactions
for any combination for which there is no entry. I think "gen-pairs" is
somewhat misleading. It doesn't generate pairs. It generates parameters for
the pairs that the user (or pdb2gmx/g_x2top) has listed, which assumes proper
use of the force field.
For a bit more discussion of how this all works:
http://lists.gromacs.org/pipermail/gmx-users/2012-December/077005.html
-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
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