[gmx-users] Constraints of distance
jalemkul at vt.edu
Wed Jun 12 02:18:17 CEST 2013
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
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.
> On Tue, Jun 11, 2013 at 6:10 PM, Justin Lemkul <jalemkul at vt.edu> 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 A. Lemkul, Ph.D.
>> Research Scientist
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
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Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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