On 6/11/13 3:47 PM, Steven Neumann wrote:
Thank you Justin. So using nrexcl 0 or 1 (should be the same with
constraints) and type 1 will allow bonded atoms to interact (vdW) with each
other?
No, there will be differences for type 1 in this case. Type 1 generates
exclusions per nrexcl. Using nrexcl = 0 will allow for all nonbonded
interactions to be calculated, but nrexcl = 1 will exclude interactions with
neighboring particles. So the combination of nrexcl = 0 with type 1
constraints, or any value of nrexcl with type 2 constraints will allow for all
nonbonded interactions to be calculated.
-Justin
On Tue, Jun 11, 2013 at 6:10 PM, Justin Lemkul <[email protected]> wrote:
On 6/11/13 10:46 AM, Steven Neumann wrote:
I was not sure about the fucntion type (1 or 2). Once in manual it is
stated that function 1 is only for exclusions and another time it can be
used to miimc bonds. Both functions are working though. Thanks anyway.
More precisely, constraints of type 1 generate exclusions between bonded
atoms within nrexcl (defined in the topology), whereas type 2 do not.
Whether or not you need the constraints to do this depends on the nature
of the force field.
-Justin
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Virginia Tech
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Department of Biochemistry
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jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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