[gmx-users] TOP file question

[Justin Lemkul]

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

-- 
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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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